6-32985503-G-C

Variant names:

• chr6-32985503-G-C
• rs3097645

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 0.92 in 152,312 control chromosomes in the GnomAD database, including 64,611 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 0.92 (64611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.920 AC: 139946 AN: 152194 Hom.: 64551 Cov.: 32

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.920 AC: 140064 AN: 152312 Hom.: 64611 Cov.: 32 AF XY: 0.919 AC XY: 68423 AN XY: 74466

African (AFR) AF: 0.978 AC: 40668 AN: 41576

American (AMR) AF: 0.886 AC: 13550 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3360 AN: 3472

East Asian (EAS) AF: 0.817 AC: 4227 AN: 5174

South Asian (SAS) AF: 0.949 AC: 4584 AN: 4828

European-Finnish (FIN) AF: 0.906 AC: 9611 AN: 10614

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60974 AN: 68026

Other (OTH) AF: 0.930 AC: 1967 AN: 2114

Alfa AF: 0.898 Hom.: 3008

Bravo AF: 0.917

Asia WGS AF: 0.911 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.39
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs3097645; hg19: chr6-32953280;