chr6-32795333-C-T

Variant names:

• chr6-32795333-C-T
• rs2621377

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 0.615 in 152,084 control chromosomes in the GnomAD database, including 28,967 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 0.62 (28967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 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: 0.615 AC: 93495 AN: 151966 Hom.: 28953 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.615 AC: 93548 AN: 152084 Hom.: 28967 Cov.: 32 AF XY: 0.620 AC XY: 46111 AN XY: 74342

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.613

Alfa AF: 0.598 Hom.: 38974

Bravo AF: 0.606

Asia WGS AF: 0.689 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2621377; hg19: chr6-32763110;