rs762534

Variant names:

• chr5-132669064-C-A
• rs762534

Your query was ambiguous. Multiple possible variants found:

• chr5-132669064-C-A
• chr5-132669064-C-T

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 0.0543 in 152,268 control chromosomes in the GnomAD database, including 279 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 0.054 (279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 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: 0.0543 AC: 8258 AN: 152150 Hom.: 280 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0966

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0429

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0543 AC: 8261 AN: 152268 Hom.: 279 Cov.: 32 AF XY: 0.0556 AC XY: 4141 AN XY: 74468

Gnomad4 AFR AF: 0.0236

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0966

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0429

Gnomad4 NFE AF: 0.0708

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0306 Hom.: 17

Bravo AF: 0.0501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.062
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs762534; hg19: chr5-132004756;