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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.270

Alfa AF: 0.248 Hom.: 735

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2856691; hg19: chr6-32653435;