rs172

Variant names:

• chr7-24995434-C-T
• rs172

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 0.752 in 152,056 control chromosomes in the GnomAD database, including 43,163 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 0.75 (43163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 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: 0.752 AC: 114212 AN: 151938 Hom.: 43127 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.752 AC: 114307 AN: 152056 Hom.: 43163 Cov.: 32 AF XY: 0.750 AC XY: 55701 AN XY: 74312

African (AFR) AF: 0.742 AC: 30775 AN: 41482

American (AMR) AF: 0.763 AC: 11663 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2542 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2788 AN: 5182

South Asian (SAS) AF: 0.816 AC: 3937 AN: 4822

European-Finnish (FIN) AF: 0.675 AC: 7103 AN: 10520

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53008 AN: 67986

Other (OTH) AF: 0.764 AC: 1608 AN: 2106

Alfa AF: 0.764 Hom.: 5746

Bravo AF: 0.754

Asia WGS AF: 0.705 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.4
DANN	Benign	0.45
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs172; hg19: chr7-25035053;