rs657075

Positions:

• chr5-132094425-G-A

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 0.0882 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0254

Gnomad4 AMR AF: 0.0723

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.0988

Gnomad4 OTH AF: 0.0836

Alfa AF: 0.101 Hom.: 1135

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

Splicing

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

Publications

LitVar

Other links and lift over

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