4-157436251-T-C

Variant names:

• chr4-157436251-T-C
• rs10517668

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 0.0892 in 152,226 control chromosomes in the GnomAD database, including 616 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 0.089 (616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 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: 0.0892 AC: 13573 AN: 152108 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0961

Gnomad ASJ AF: 0.0497

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0892

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0892 AC: 13581 AN: 152226 Hom.: 616 Cov.: 32 AF XY: 0.0883 AC XY: 6571 AN XY: 74432

African (AFR) AF: 0.0808 AC: 3356 AN: 41528

American (AMR) AF: 0.0960 AC: 1468 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0497 AC: 172 AN: 3464

East Asian (EAS) AF: 0.158 AC: 817 AN: 5176

South Asian (SAS) AF: 0.0885 AC: 427 AN: 4826

European-Finnish (FIN) AF: 0.0813 AC: 862 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0904 AC: 6146 AN: 68018

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0873 Hom.: 1120

Bravo AF: 0.0906

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.6
DANN	Benign	0.36
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10517668; hg19: chr4-158357403;