rs2856691

chr6-32685658-G-Achr6-32685658-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;