chr4-15934137-G-T

Variant names:

• chr4-15934137-G-T
• rs2532095

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 0.833 in 152,094 control chromosomes in the GnomAD database, including 53,165 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 0.83 (53165 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.864 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: 0.833 AC: 126602 AN: 151976 Hom.: 53136 Cov.: 30

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.833 AC: 126679 AN: 152094 Hom.: 53165 Cov.: 30 AF XY: 0.833 AC XY: 61934 AN XY: 74372

African (AFR) AF: 0.798 AC: 33087 AN: 41454

American (AMR) AF: 0.771 AC: 11776 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2962 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3092 AN: 5154

South Asian (SAS) AF: 0.817 AC: 3930 AN: 4812

European-Finnish (FIN) AF: 0.929 AC: 9858 AN: 10608

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.869 AC: 59119 AN: 67998

Other (OTH) AF: 0.832 AC: 1756 AN: 2110

Alfa AF: 0.853 Hom.: 72018

Bravo AF: 0.822

Asia WGS AF: 0.679 AC: 2363 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.82
DANN	Benign	0.69
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2532095; hg19: chr4-15935760;