4-179212588-C-T

Variant names:

• chr4-179212588-C-T
• rs1457402

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 0.0901 in 152,114 control chromosomes in the GnomAD database, including 710 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 0.090 (710 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690
• Publications: 0 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 (SAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0902 AC: 13703 AN: 151996 Hom.: 711 Cov.: 33

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0748

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

GnomAD4 genome AF: 0.0901 AC: 13707 AN: 152114 Hom.: 710 Cov.: 33 AF XY: 0.0919 AC XY: 6829 AN XY: 74336

African (AFR) AF: 0.0723 AC: 2999 AN: 41506

American (AMR) AF: 0.131 AC: 2005 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3472

East Asian (EAS) AF: 0.133 AC: 688 AN: 5172

South Asian (SAS) AF: 0.143 AC: 689 AN: 4818

European-Finnish (FIN) AF: 0.0733 AC: 776 AN: 10580

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5898 AN: 67988

Other (OTH) AF: 0.0740 AC: 156 AN: 2108

Alfa AF: 0.0863 Hom.: 1868

Bravo AF: 0.0923

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.96
DANN	Benign	0.51
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1457402; hg19: chr4-180133742;