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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.634

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2621403; hg19: chr6-32749795;