13-20193244-A-G

Variant names:

• chr13-20193244-A-G
• rs9550621
• ENST00000736390.1:n.231+1211T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000736390.1(ENSG00000296095):​n.231+1211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,084 control chromosomes in the GnomAD database, including 55,848 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.83 (55848 hom., cov: 33)
• Consequence: ENSG00000296095 ENST00000736390.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

Genes affected

ENSG00000296095 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 13-20193244-A-G is Benign according to our data. Variant chr13-20193244-A-G is described in ClinVar as Benign. ClinVar VariationId is 1247342.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296095	ENST00000736390.1	n.231+1211T>C		intron_variant	Intron 1 of 3
ENSG00000296095	ENST00000736391.1	n.*149T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126581 AN: 151970 Hom.: 55843 Cov.: 33

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.867

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.833 AC: 126623 AN: 152084 Hom.: 55848 Cov.: 33 AF XY: 0.836 AC XY: 62178 AN XY: 74334

African (AFR) AF: 0.508 AC: 21059 AN: 41464

American (AMR) AF: 0.908 AC: 13893 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3231 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5119 AN: 5124

South Asian (SAS) AF: 0.967 AC: 4661 AN: 4820

European-Finnish (FIN) AF: 0.964 AC: 10233 AN: 10620

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65474 AN: 67970

Other (OTH) AF: 0.868 AC: 1833 AN: 2112

Alfa AF: 0.886 Hom.: 7690

Bravo AF: 0.813

Asia WGS AF: 0.952 AC: 3310 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.3
DANN	Benign	0.21
PhyloP100		-1.0
PromoterAI		0.012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9550621; hg19: chr13-20767383;