6-32714531-C-A

Variant names:

• chr6-32714531-C-A
• rs3104405

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 0.649 in 151,884 control chromosomes in the GnomAD database, including 32,405 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 (32405 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.62
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 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: 0.649 AC: 98508 AN: 151766 Hom.: 32393 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.649 AC: 98569 AN: 151884 Hom.: 32405 Cov.: 32 AF XY: 0.645 AC XY: 47849 AN XY: 74188

African (AFR) AF: 0.575 AC: 23802 AN: 41388

American (AMR) AF: 0.730 AC: 11153 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2736 AN: 3472

East Asian (EAS) AF: 0.747 AC: 3872 AN: 5180

South Asian (SAS) AF: 0.790 AC: 3801 AN: 4814

European-Finnish (FIN) AF: 0.508 AC: 5328 AN: 10492

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45643 AN: 67952

Other (OTH) AF: 0.695 AC: 1466 AN: 2110

Alfa AF: 0.677 Hom.: 47265

Bravo AF: 0.663

Asia WGS AF: 0.790 AC: 2746 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.26
DANN	Benign	0.25
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs3104405; hg19: chr6-32682308;