chr7-24995434-C-T

Variant names:

• chr7-24995434-C-T
• rs172

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 0.752 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.764

Alfa AF: 0.766 Hom.: 5539

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs172; hg19: chr7-25035053;