5-132665694-G-A

Position:

• chr5-132665694-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 0.115 in 152,226 control chromosomes in the GnomAD database, including 1,276 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 0.11 (1276 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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: 0.115 AC: 17443 AN: 152108 Hom.: 1273 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.115 AC: 17475 AN: 152226 Hom.: 1276 Cov.: 33 AF XY: 0.114 AC XY: 8496 AN XY: 74434

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0511

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0909 Hom.: 440

Bravo AF: 0.123

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243210; hg19: chr5-132001386;