rs7594674

Positions:

• chr2-67052828-G-A
• chr2-67052828-G-C
• chr2-67052828-G-T

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 0.716 in 148,908 control chromosomes in the GnomAD database, including 38,295 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 0.72 (38295 hom., cov: 24)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67052828G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.716 AC: 106564 AN: 148822 Hom.: 38287 Cov.: 24

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.716 AC: 106612 AN: 148908 Hom.: 38295 Cov.: 24 AF XY: 0.714 AC XY: 51693 AN XY: 72448

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.722

Alfa AF: 0.652 Hom.: 3349

Bravo AF: 0.715

Asia WGS AF: 0.773 AC: 2682 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.5
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: rs7594674; hg19: chr2-67279960;