5-132406536-G-C

Variant names:

• chr5-132406536-G-C
• rs6596075

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.750 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

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.782

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6596075; hg19: chr5-131742228;