rs2894401

Variant names:

• chr6-35441182-A-G
• rs2894401
• ENST00000794874.1:n.116-1862A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000794874.1(ENSG00000303476):​n.116-1862A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000303476 ENST00000794874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 14 publications found

Genes affected

ENSG00000303476 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303476	ENST00000794874.1	n.116-1862A>G		intron_variant	Intron 1 of 7
ENSG00000303476	ENST00000794875.1	n.99-1862A>G		intron_variant	Intron 1 of 6
ENSG00000303476	ENST00000794876.1	n.99-1862A>G		intron_variant	Intron 1 of 6

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

African (AFR) AF: 0.863 AC: 35783 AN: 41474

American (AMR) AF: 0.760 AC: 11620 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3470

East Asian (EAS) AF: 0.693 AC: 3577 AN: 5162

South Asian (SAS) AF: 0.782 AC: 3769 AN: 4822

European-Finnish (FIN) AF: 0.784 AC: 8296 AN: 10576

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48430 AN: 67970

Other (OTH) AF: 0.737 AC: 1557 AN: 2114

Alfa AF: 0.725 Hom.: 80989

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2894401; hg19: chr6-35408959;