rs7594976

Positions:

• chr2-8702365-G-A

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 0.0564 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

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 = 0.132 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: 0.0562 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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0654

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.0709

Gnomad4 FIN AF: 0.0147

Gnomad4 NFE AF: 0.0104

Gnomad4 OTH AF: 0.0526

Alfa AF: 0.0371 Hom.: 108

Bravo AF: 0.0619

Asia WGS AF: 0.107 AC: 371 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	0.078
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7594976; hg19: chr2-8842495;