rs665808

Variant names:

• chr13-48911777-T-C
• rs665808
• ENST00000776192.1:n.348+956A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000776192.1(ENSG00000301102):​n.348+956A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,882 control chromosomes in the GnomAD database, including 20,900 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (20900 hom., cov: 31)
• Consequence: ENSG00000301102 ENST00000776192.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 2 publications found

Genes affected

ENSG00000301102 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 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
ENSG00000301102	ENST00000776192.1	n.348+956A>G		intron_variant	Intron 3 of 3
ENSG00000301102	ENST00000776193.1	n.376+956A>G		intron_variant	Intron 3 of 3
ENSG00000301102	ENST00000776194.1	n.348+956A>G		intron_variant	Intron 3 of 3
ENSG00000301102	ENST00000776195.1	n.423+956A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75155 AN: 151764 Hom.: 20907 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.495 AC: 75161 AN: 151882 Hom.: 20900 Cov.: 31 AF XY: 0.498 AC XY: 36965 AN XY: 74238

African (AFR) AF: 0.231 AC: 9585 AN: 41422

American (AMR) AF: 0.535 AC: 8157 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2074 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2005 AN: 5154

South Asian (SAS) AF: 0.564 AC: 2715 AN: 4816

European-Finnish (FIN) AF: 0.613 AC: 6461 AN: 10544

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.624 AC: 42399 AN: 67922

Other (OTH) AF: 0.514 AC: 1083 AN: 2108

Alfa AF: 0.587 Hom.: 13711

Bravo AF: 0.474

Asia WGS AF: 0.450 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.52
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs665808; hg19: chr13-49485913; COSMIC: COSV56526730;