rs4759915

Positions:

• chr12-131327953-G-A
• chr12-131327953-G-C

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 0.457 in 151,790 control chromosomes in the GnomAD database, including 16,505 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 0.46 (16505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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: 0.457 AC: 69260 AN: 151672 Hom.: 16483 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.457 AC: 69313 AN: 151790 Hom.: 16505 Cov.: 32 AF XY: 0.462 AC XY: 34288 AN XY: 74160

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.466

Alfa AF: 0.456 Hom.: 8870

Bravo AF: 0.460

Asia WGS AF: 0.569 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.49
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4759915; hg19: chr12-131812498;