rs792173

Variant names:

• chr7-125598954-C-G
• rs792173

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 0.0876 in 151,626 control chromosomes in the GnomAD database, including 1,825 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 0.088 (1825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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: 0.0874 AC: 13239 AN: 151506 Hom.: 1819 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00230

Gnomad FIN AF: 0.000765

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00729

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0876 AC: 13286 AN: 151626 Hom.: 1825 Cov.: 32 AF XY: 0.0838 AC XY: 6205 AN XY: 74072

African (AFR) AF: 0.290 AC: 11997 AN: 41352

American (AMR) AF: 0.0390 AC: 593 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.00923 AC: 32 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5134

South Asian (SAS) AF: 0.00188 AC: 9 AN: 4788

European-Finnish (FIN) AF: 0.000765 AC: 8 AN: 10456

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00729 AC: 495 AN: 67912

Other (OTH) AF: 0.0688 AC: 145 AN: 2108

Alfa AF: 0.0570 Hom.: 147

Bravo AF: 0.100

Asia WGS AF: 0.0200 AC: 69 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.62
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs792173; hg19: chr7-125239008;