rs762534

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;