rs4726160

Variant names:

• chr7-152462421-T-C
• rs4726160

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 0.433 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.640 AC: 26521 AN: 41430

American (AMR) AF: 0.384 AC: 5867 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1373 AN: 3472

East Asian (EAS) AF: 0.184 AC: 950 AN: 5166

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4820

European-Finnish (FIN) AF: 0.378 AC: 3987 AN: 10556

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24414 AN: 67920

Other (OTH) AF: 0.431 AC: 911 AN: 2112

Alfa AF: 0.376 Hom.: 6381

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4726160; hg19: chr7-152159506;