rs2894401

Positions:

• chr6-35441182-A-G

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 0.763 in 152,074 control chromosomes in the GnomAD database, including 44,709 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 0.76 (44709 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 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: 0.763 AC: 115973 AN: 151956 Hom.: 44656 Cov.: 31

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.763 AC: 116089 AN: 152074 Hom.: 44709 Cov.: 31 AF XY: 0.766 AC XY: 56910 AN XY: 74332

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.737

Alfa AF: 0.721 Hom.: 58071

Bravo AF: 0.766

Asia WGS AF: 0.742 AC: 2579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2894401; hg19: chr6-35408959;