chr18-55275753-C-G

Variant names:

• chr18-55275753-C-G
• rs587784466
• NM_001083962.2:c.656-1G>C

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_001083962.2(TCF4):​c.656-1G>C variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TCF4 NM_001083962.2 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.24
• Publications: 0 publications found

Genes affected

TCF4 (HGNC:11634): (transcription factor 4) This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor. The encoded protein recognizes an Ephrussi-box ('E-box') binding site ('CANNTG') - a motif first identified in immunoglobulin enhancers. This gene is broadly expressed, and may play an important role in nervous system development. Defects in this gene are a cause of Pitt-Hopkins syndrome. In addition, an intronic CTG repeat normally numbering 10-37 repeat units can expand to >50 repeat units and cause Fuchs endothelial corneal dystrophy. Multiple alternatively spliced transcript variants that encode different proteins have been described. [provided by RefSeq, Jul 2016]

TCF4 Gene-Disease associations (from GenCC):

• Pitt-Hopkins syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, G2P, ClinGen
• corneal dystrophy, Fuchs endothelial, 3

  Inheritance: AD Classification: STRONG Submitted by: G2P
• autosomal dominant non-syndromic intellectual disability

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Fuchs' endothelial dystrophy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• intellectual disability

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 18-55275753-C-G is Pathogenic according to our data. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-55275753-C-G is described in CliVar as Pathogenic. Clinvar id is 160087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCF4	NM_001083962.2	c.656-1G>C		splice_acceptor_variant, intron_variant	Intron 9 of 19	ENST00000354452.8	NP_001077431.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCF4	ENST00000354452.8	c.656-1G>C		splice_acceptor_variant, intron_variant	Intron 9 of 19	5	NM_001083962.2	ENSP00000346440.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Pitt-Hopkins syndrome Pathogenic:2

May 01, 2007

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.37
CADD	Pathogenic	34
DANN	Uncertain	1.0
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.1
FATHMM_MKL	Pathogenic	0.98	D
PhyloP100		7.2
GERP RS		5.9
PromoterAI		0.0068	Neutral
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.99		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587784466; hg19: chr18-52942984;