chr5-132094425-G-A

Variant names:

• chr5-132094425-G-A
• rs657075

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 0.0882 in 152,246 control chromosomes in the GnomAD database, including 850 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 0.088 (850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.984
• Publications: 47 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 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: 0.0883 AC: 13434 AN: 152126 Hom.: 852 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0724

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.0825

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

GnomAD4 genome AF: 0.0882 AC: 13433 AN: 152246 Hom.: 850 Cov.: 32 AF XY: 0.0924 AC XY: 6874 AN XY: 74428

African (AFR) AF: 0.0254 AC: 1058 AN: 41574

American (AMR) AF: 0.0723 AC: 1107 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1508 AN: 5164

South Asian (SAS) AF: 0.113 AC: 542 AN: 4810

European-Finnish (FIN) AF: 0.164 AC: 1737 AN: 10596

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0988 AC: 6722 AN: 68014

Other (OTH) AF: 0.0836 AC: 176 AN: 2106

Alfa AF: 0.0979 Hom.: 3026

Bravo AF: 0.0778

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.53
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs657075; hg19: chr5-131430118; COSMIC: COSV50498876;