rs6906021

Positions:

• chr6-32658534-T-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 0.47 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

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 (SAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.504

Alfa AF: 0.473 Hom.: 14033

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6906021; hg19: chr6-32626311;