rs2621403

Variant names:

• chr6-32782018-T-A
• rs2621403

Your query was ambiguous. Multiple possible variants found:

• chr6-32782018-T-A
• chr6-32782018-T-C

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 0.647 in 151,900 control chromosomes in the GnomAD database, including 31,913 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 0.65 (31913 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 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: 0.647 AC: 98256 AN: 151782 Hom.: 31892 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.647 AC: 98321 AN: 151900 Hom.: 31913 Cov.: 31 AF XY: 0.652 AC XY: 48381 AN XY: 74244

African (AFR) AF: 0.650 AC: 26981 AN: 41488

American (AMR) AF: 0.624 AC: 9516 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2253 AN: 3464

East Asian (EAS) AF: 0.735 AC: 3789 AN: 5158

South Asian (SAS) AF: 0.726 AC: 3475 AN: 4784

European-Finnish (FIN) AF: 0.703 AC: 7413 AN: 10546

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42665 AN: 67894

Other (OTH) AF: 0.634 AC: 1339 AN: 2112

Alfa AF: 0.648 Hom.: 3993

Bravo AF: 0.640

Asia WGS AF: 0.740 AC: 2572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.33
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2621403; hg19: chr6-32749795;