rs6502762

Variant names:

• chr17-3968970-C-T
• rs6502762

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 0.376 in 151,974 control chromosomes in the GnomAD database, including 11,241 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 0.38 (11241 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57142 AN: 151856 Hom.: 11213 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.376 AC: 57216 AN: 151974 Hom.: 11241 Cov.: 31 AF XY: 0.371 AC XY: 27558 AN XY: 74246

African (AFR) AF: 0.476 AC: 19742 AN: 41448

American (AMR) AF: 0.413 AC: 6317 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1485 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1336 AN: 5162

South Asian (SAS) AF: 0.254 AC: 1221 AN: 4814

European-Finnish (FIN) AF: 0.253 AC: 2664 AN: 10524

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23140 AN: 67964

Other (OTH) AF: 0.359 AC: 756 AN: 2106

Alfa AF: 0.345 Hom.: 4831

Bravo AF: 0.393

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.82
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6502762; hg19: chr17-3872264; COSMIC: COSV59227597;