rs12585734

Variant names:

• chr13-76293531-G-A
• rs12585734

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 0.054 in 152,022 control chromosomes in the GnomAD database, including 382 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 (382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

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 (EAS) allele frequency at 95% confidence interval = 0.231 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: 0.0539 AC: 8190 AN: 151904 Hom.: 377 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.0818

Gnomad FIN AF: 0.0808

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0505

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

GnomAD4 genome AF: 0.0540 AC: 8208 AN: 152022 Hom.: 382 Cov.: 32 AF XY: 0.0562 AC XY: 4172 AN XY: 74300

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0658

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.0811

Gnomad4 FIN AF: 0.0808

Gnomad4 NFE AF: 0.0564

Gnomad4 OTH AF: 0.0571

Alfa AF: 0.0573 Hom.: 319

Bravo AF: 0.0549

Asia WGS AF: 0.161 AC: 557 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12585734; hg19: chr13-76867667; COSMIC: COSV69365756;