rs2621403

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;