rs7594976

Variant names:

• chr2-8702365-G-A
• rs7594976
• ENST00000825042.1:n.121-777G>A

Variant summary

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

The ENST00000825042.1(ENSG00000307315):​n.121-777G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,200 control chromosomes in the GnomAD database, including 522 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 0.056 (522 hom., cov: 32)
• Consequence: ENSG00000307315 ENST00000825042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 2 publications found

Genes affected

ENSG00000307315 (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 = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825042.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307315	ENST00000825042.1		n.121-777G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0562 AC: 8547 AN: 152082 Hom.: 517 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0564 AC: 8586 AN: 152200 Hom.: 522 Cov.: 32 AF XY: 0.0584 AC XY: 4346 AN XY: 74422

African (AFR) AF: 0.135 AC: 5600 AN: 41484

American (AMR) AF: 0.0654 AC: 1001 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3472

East Asian (EAS) AF: 0.106 AC: 550 AN: 5172

South Asian (SAS) AF: 0.0709 AC: 342 AN: 4826

European-Finnish (FIN) AF: 0.0147 AC: 156 AN: 10604

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0104 AC: 707 AN: 68020

Other (OTH) AF: 0.0526 AC: 111 AN: 2110

Alfa AF: 0.0368 Hom.: 120

Bravo AF: 0.0619

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.078
DANN	Benign	0.63
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs7594976; hg19: chr2-8842495;