6-32695854-T-C

Variant names:

• chr6-32695854-T-C
• rs3129720

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 0.762 in 151,662 control chromosomes in the GnomAD database, including 44,267 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 0.76 (44267 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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: 0.762 AC: 115494 AN: 151544 Hom.: 44239 Cov.: 29

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.762 AC: 115579 AN: 151662 Hom.: 44267 Cov.: 29 AF XY: 0.764 AC XY: 56568 AN XY: 74086

African (AFR) AF: 0.719 AC: 29720 AN: 41360

American (AMR) AF: 0.813 AC: 12386 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2919 AN: 3466

East Asian (EAS) AF: 0.905 AC: 4676 AN: 5166

South Asian (SAS) AF: 0.882 AC: 4237 AN: 4806

European-Finnish (FIN) AF: 0.750 AC: 7851 AN: 10472

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.753 AC: 51090 AN: 67850

Other (OTH) AF: 0.799 AC: 1682 AN: 2104

Alfa AF: 0.755 Hom.: 80681

Bravo AF: 0.767

Asia WGS AF: 0.884 AC: 3073 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.45
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs3129720; hg19: chr6-32663631;