6-32684117-A-G

Variant names:

• chr6-32684117-A-G
• rs2856695

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 0.504 in 152,030 control chromosomes in the GnomAD database, including 19,712 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 0.50 (19712 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 14 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 = 0.661 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: 0.504 AC: 76610 AN: 151912 Hom.: 19703 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.504 AC: 76656 AN: 152030 Hom.: 19712 Cov.: 32 AF XY: 0.505 AC XY: 37561 AN XY: 74318

African (AFR) AF: 0.469 AC: 19441 AN: 41426

American (AMR) AF: 0.612 AC: 9360 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2191 AN: 3472

East Asian (EAS) AF: 0.679 AC: 3516 AN: 5176

South Asian (SAS) AF: 0.551 AC: 2656 AN: 4824

European-Finnish (FIN) AF: 0.447 AC: 4716 AN: 10554

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32955 AN: 67972

Other (OTH) AF: 0.538 AC: 1137 AN: 2114

Alfa AF: 0.508 Hom.: 16792

Bravo AF: 0.521

Asia WGS AF: 0.604 AC: 2100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.46
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2856695; hg19: chr6-32651894;