chr4-157457621-T-C

Variant names:

• chr4-157457621-T-C
• rs17036150

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 0.172 in 151,114 control chromosomes in the GnomAD database, including 2,300 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 0.17 (2300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 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: 0.173 AC: 26058 AN: 150994 Hom.: 2299 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.172 AC: 26067 AN: 151114 Hom.: 2300 Cov.: 32 AF XY: 0.173 AC XY: 12784 AN XY: 73878

African (AFR) AF: 0.151 AC: 6126 AN: 40548

American (AMR) AF: 0.161 AC: 2458 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3470

East Asian (EAS) AF: 0.177 AC: 916 AN: 5180

South Asian (SAS) AF: 0.147 AC: 707 AN: 4824

European-Finnish (FIN) AF: 0.192 AC: 2025 AN: 10570

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12626 AN: 67960

Other (OTH) AF: 0.186 AC: 391 AN: 2102

Alfa AF: 0.164 Hom.: 354

Bravo AF: 0.169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs17036150; hg19: chr4-158378773;