rs4726160

chr7-152462421-T-C

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 0.433 in 151,944 control chromosomes in the GnomAD database, including 15,606 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 0.43 (15606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65718 AN: 151826 Hom.: 15588 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.433 AC: 65786 AN: 151944 Hom.: 15606 Cov.: 32 AF XY: 0.428 AC XY: 31788 AN XY: 74280

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.431

Alfa AF: 0.377 Hom.: 5839

Bravo AF: 0.444

Asia WGS AF: 0.264 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.5
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4726160; hg19: chr7-152159506;