4-156976632-T-G

Variant names:

• chr4-156976632-T-G
• rs13133399

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 0.137 in 152,150 control chromosomes in the GnomAD database, including 1,574 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 0.14 (1574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20831 AN: 152032 Hom.: 1572 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.137 AC: 20838 AN: 152150 Hom.: 1574 Cov.: 32 AF XY: 0.139 AC XY: 10367 AN XY: 74416

African (AFR) AF: 0.129 AC: 5345 AN: 41516

American (AMR) AF: 0.118 AC: 1801 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1378 AN: 5152

South Asian (SAS) AF: 0.233 AC: 1121 AN: 4818

European-Finnish (FIN) AF: 0.122 AC: 1291 AN: 10602

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

European-Non Finnish (NFE) AF: 0.132 AC: 8944 AN: 67980

Other (OTH) AF: 0.132 AC: 279 AN: 2116

Alfa AF: 0.0727 Hom.: 91

Bravo AF: 0.135

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.3
DANN	Benign	0.83
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs13133399; hg19: chr4-157897784;