rs2621383

Variant names:

• chr6-32791558-C-A
• rs2621383

Your query was ambiguous. Multiple possible variants found:

• chr6-32791558-C-A
• chr6-32791558-C-G
• chr6-32791558-C-T

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 0.654 in 151,886 control chromosomes in the GnomAD database, including 32,596 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 (32596 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.654 AC: 99250 AN: 151768 Hom.: 32577 Cov.: 30

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.654 AC: 99310 AN: 151886 Hom.: 32596 Cov.: 30 AF XY: 0.658 AC XY: 48859 AN XY: 74228

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.651

Alfa AF: 0.644 Hom.: 9719

Bravo AF: 0.647

Asia WGS AF: 0.760 AC: 2639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2621383; hg19: chr6-32759335;