rs2856691

Variant names:

• chr6-32685658-G-A
• rs2856691

Your query was ambiguous. Multiple possible variants found:

• chr6-32685658-G-A
• chr6-32685658-G-C

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 0.254 in 148,942 control chromosomes in the GnomAD database, including 5,002 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 0.25 (5002 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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: 0.253 AC: 37724 AN: 148820 Hom.: 4997 Cov.: 30

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.254 AC: 37757 AN: 148942 Hom.: 5002 Cov.: 30 AF XY: 0.260 AC XY: 18884 AN XY: 72738

African (AFR) AF: 0.212 AC: 8573 AN: 40370

American (AMR) AF: 0.379 AC: 5620 AN: 14846

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1177 AN: 3436

East Asian (EAS) AF: 0.346 AC: 1706 AN: 4936

South Asian (SAS) AF: 0.351 AC: 1646 AN: 4696

European-Finnish (FIN) AF: 0.266 AC: 2745 AN: 10338

Middle Eastern (MID) AF: 0.264 AC: 75 AN: 284

European-Non Finnish (NFE) AF: 0.230 AC: 15460 AN: 67098

Other (OTH) AF: 0.270 AC: 551 AN: 2044

Alfa AF: 0.295 Hom.: 4409

Bravo AF: 0.262

Asia WGS AF: 0.281 AC: 976 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.25
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2856691; hg19: chr6-32653435;