14-54941691-C-T

Variant names:

• chr14-54941691-C-T
• rs1595047164
• NM_007086.4:c.3190-1G>A

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Strong PM2

The NM_007086.4(WDHD1):​c.3190-1G>A variant causes a splice acceptor, intron change. 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 Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: WDHD1 NM_007086.4 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.74

Genes affected

WDHD1 (HGNC:23170): (WD repeat and HMG-box DNA binding protein 1) The protein encoded by this gene contains multiple N-terminal WD40 domains and a C-terminal high mobility group (HMG) box. WD40 domains are found in a variety of eukaryotic proteins and may function as adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly. HMG boxes are found in many eukaryotic proteins involved in chromatin assembly, transcription and replication. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.8088496 fraction of the gene.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDHD1	NM_007086.4	c.3190-1G>A		splice_acceptor_variant, intron_variant	Intron 25 of 25	ENST00000360586.8	NP_009017.1
WDHD1	NM_001008396.3	c.2821-1G>A		splice_acceptor_variant, intron_variant	Intron 24 of 24		NP_001008397.1
WDHD1	XM_006720012.2	c.3184-1G>A		splice_acceptor_variant, intron_variant	Intron 25 of 25		XP_006720075.1
WDHD1	XM_011536373.3	c.2101-1G>A		splice_acceptor_variant, intron_variant	Intron 16 of 16		XP_011534675.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDHD1	ENST00000360586.8	c.3190-1G>A		splice_acceptor_variant, intron_variant	Intron 25 of 25	1	NM_007086.4	ENSP00000353793.3
WDHD1	ENST00000420358.2	c.2821-1G>A		splice_acceptor_variant, intron_variant	Intron 24 of 24	5		ENSP00000399349.2
WDHD1	ENST00000475379.1	n.277-1G>A		splice_acceptor_variant, intron_variant	Intron 1 of 1	2
WDHD1	ENST00000567693.1	n.*1640-1G>A		splice_acceptor_variant, intron_variant	Intron 13 of 13	2		ENSP00000456806.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Mar 01, 2019

CeGaT Center for Human Genetics Tuebingen

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.23	D
BayesDel_noAF	Uncertain	0.10
CADD	Pathogenic	33
DANN	Uncertain	0.99
Eigen	Pathogenic	0.95
Eigen_PC	Pathogenic	0.75
FATHMM_MKL	Pathogenic	0.98	D
GERP RS		5.4

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.83
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.93		Position offset: -2
DS_AL_spliceai		0.99		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs1595047164; hg19: chr14-55408409;