rs12585734

chr13-76293531-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 0.054 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/exons	MANE	UniProt

Ensembl

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