chr5-132406536-G-C

Variant names:

• chr5-132406536-G-C
• rs6596075

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 0.75 in 152,104 control chromosomes in the GnomAD database, including 44,624 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 0.75 (44624 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 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: 0.750 AC: 114002 AN: 151984 Hom.: 44627 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.750 AC: 114029 AN: 152104 Hom.: 44624 Cov.: 31 AF XY: 0.754 AC XY: 56040 AN XY: 74358

African (AFR) AF: 0.500 AC: 20729 AN: 41446

American (AMR) AF: 0.810 AC: 12375 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3472

East Asian (EAS) AF: 0.910 AC: 4707 AN: 5170

South Asian (SAS) AF: 0.832 AC: 4019 AN: 4830

European-Finnish (FIN) AF: 0.869 AC: 9205 AN: 10592

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.843 AC: 57343 AN: 68004

Other (OTH) AF: 0.782 AC: 1646 AN: 2106

Alfa AF: 0.824 Hom.: 25743

Bravo AF: 0.736

Asia WGS AF: 0.803 AC: 2791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.60
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6596075; hg19: chr5-131742228;