rs6906021

Variant names:

• chr6-32658534-T-C
• rs6906021

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 0.47 in 151,004 control chromosomes in the GnomAD database, including 17,173 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 0.47 (17173 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.01
• Publications: 62 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 (SAS) allele frequency at 95% confidence interval = 0.551 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: 0.470 AC: 70947 AN: 150888 Hom.: 17174 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.470 AC: 70974 AN: 151004 Hom.: 17173 Cov.: 31 AF XY: 0.466 AC XY: 34427 AN XY: 73846

African (AFR) AF: 0.497 AC: 20439 AN: 41148

American (AMR) AF: 0.460 AC: 6987 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1722 AN: 3456

East Asian (EAS) AF: 0.509 AC: 2621 AN: 5150

South Asian (SAS) AF: 0.569 AC: 2716 AN: 4772

European-Finnish (FIN) AF: 0.360 AC: 3775 AN: 10486

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31209 AN: 67520

Other (OTH) AF: 0.504 AC: 1051 AN: 2086

Alfa AF: 0.469 Hom.: 52985

Bravo AF: 0.479

Asia WGS AF: 0.565 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.087
DANN	Benign	0.54
PhyloP100		-6.0

Splicing

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

Other links and lift over

dbSNP: rs6906021; hg19: chr6-32626311;