rs12982559

chr19-54713574-A-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 0.745 in 158,124 control chromosomes in the GnomAD database, including 44,509 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 0.75 (42953 hom., cov: 31)
  • Exomes 𝑓: 0.71 (1556 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.746 AC: 113354 AN: 151900 Hom.: 42902 Cov.: 31

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.725

GnomAD4 exome AF: 0.709 AC: 4331 AN: 6106 Hom.: 1556 AF XY: 0.720 AC XY: 2279 AN XY: 3166

Gnomad4 AFR exome AF: 0.841

Gnomad4 AMR exome AF: 0.818

Gnomad4 ASJ exome AF: 0.689

Gnomad4 EAS exome AF: 0.983

Gnomad4 SAS exome AF: 0.735

Gnomad4 FIN exome AF: 0.674

Gnomad4 NFE exome AF: 0.685

Gnomad4 OTH exome AF: 0.686

GnomAD4 genome AF: 0.746 AC: 113466 AN: 152018 Hom.: 42953 Cov.: 31 AF XY: 0.748 AC XY: 55570 AN XY: 74298

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.726

Alfa AF: 0.687 Hom.: 41066

Bravo AF: 0.757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12982559; hg19: chr19-55225076;