7-125892952-G-C

Variant names:

• chr7-125892952-G-C
• rs6947579

Variant summary

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

The variant allele was found at a frequency of 0.72 in 152,080 control chromosomes in the GnomAD database, including 40,116 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 (40116 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 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

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109431 AN: 151960 Hom.: 40085 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.720 AC: 109505 AN: 152080 Hom.: 40116 Cov.: 33 AF XY: 0.720 AC XY: 53577 AN XY: 74366

African (AFR) AF: 0.847 AC: 35158 AN: 41498

American (AMR) AF: 0.559 AC: 8540 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2141 AN: 3470

East Asian (EAS) AF: 0.696 AC: 3599 AN: 5174

South Asian (SAS) AF: 0.631 AC: 3037 AN: 4812

European-Finnish (FIN) AF: 0.780 AC: 8247 AN: 10572

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46484 AN: 67964

Other (OTH) AF: 0.682 AC: 1437 AN: 2106

Alfa AF: 0.704 Hom.: 4479

Bravo AF: 0.706

Asia WGS AF: 0.666 AC: 2312 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.46
DANN	Benign	0.72
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs6947579; hg19: chr7-125533006;