chr6-32808637-T-A

Variant names:

• chr6-32808637-T-A
• rs2857130

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 152,104 control chromosomes in the GnomAD database, including 34,500 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 (34500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 20 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 = 0.783 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: 0.671 AC: 102048 AN: 151986 Hom.: 34493 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.671 AC: 102092 AN: 152104 Hom.: 34500 Cov.: 32 AF XY: 0.678 AC XY: 50428 AN XY: 74364

African (AFR) AF: 0.647 AC: 26847 AN: 41474

American (AMR) AF: 0.653 AC: 9974 AN: 15284

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

East Asian (EAS) AF: 0.718 AC: 3715 AN: 5176

South Asian (SAS) AF: 0.804 AC: 3872 AN: 4818

European-Finnish (FIN) AF: 0.769 AC: 8145 AN: 10594

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44658 AN: 67966

Other (OTH) AF: 0.682 AC: 1442 AN: 2114

Alfa AF: 0.664 Hom.: 18671

Bravo AF: 0.657

Asia WGS AF: 0.741 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.8
DANN	Benign	0.39
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2857130; hg19: chr6-32776414;