rs1338657

Variant names:

• chr6-102401461-C-T
• rs1338657

Variant summary

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

The variant allele was found at a frequency of 0.422 in 151,602 control chromosomes in the GnomAD database, including 13,831 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 0.42 (13831 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.422 AC: 63883 AN: 151482 Hom.: 13814 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.422 AC: 63938 AN: 151602 Hom.: 13831 Cov.: 31 AF XY: 0.426 AC XY: 31563 AN XY: 74046

African (AFR) AF: 0.347 AC: 14377 AN: 41414

American (AMR) AF: 0.518 AC: 7867 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3464

East Asian (EAS) AF: 0.576 AC: 2942 AN: 5110

South Asian (SAS) AF: 0.490 AC: 2363 AN: 4824

European-Finnish (FIN) AF: 0.435 AC: 4568 AN: 10510

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28685 AN: 67798

Other (OTH) AF: 0.439 AC: 921 AN: 2100

Alfa AF: 0.429 Hom.: 20473

Bravo AF: 0.425

Asia WGS AF: 0.516 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1338657; hg19: chr6-102849336; COSMIC: COSV69416457;