6-32807909-A-G

Variant names:

• chr6-32807909-A-G
• rs2857136

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 0.671 in 152,152 control chromosomes in the GnomAD database, including 34,499 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 0.67 (34499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.671 AC: 102054 AN: 152034 Hom.: 34492 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.671 AC: 102098 AN: 152152 Hom.: 34499 Cov.: 32 AF XY: 0.678 AC XY: 50416 AN XY: 74382

African (AFR) AF: 0.647 AC: 26839 AN: 41476

American (AMR) AF: 0.653 AC: 9980 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2461 AN: 3472

East Asian (EAS) AF: 0.718 AC: 3716 AN: 5174

South Asian (SAS) AF: 0.803 AC: 3876 AN: 4828

European-Finnish (FIN) AF: 0.768 AC: 8145 AN: 10604

Middle Eastern (MID) AF: 0.786 AC: 228 AN: 290

European-Non Finnish (NFE) AF: 0.657 AC: 44665 AN: 67990

Other (OTH) AF: 0.682 AC: 1441 AN: 2114

Alfa AF: 0.665 Hom.: 19462

Bravo AF: 0.657

Asia WGS AF: 0.741 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.88
DANN	Benign	0.33
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2857136; hg19: chr6-32775686;