rs12984174

chr19-18021731-T-Cchr19-18021731-T-G

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 0.115 in 151,854 control chromosomes in the GnomAD database, including 1,085 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 0.11 (1085 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 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: 0.115 AC: 17392 AN: 151736 Hom.: 1081 Cov.: 30

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.115 AC: 17407 AN: 151854 Hom.: 1085 Cov.: 30 AF XY: 0.114 AC XY: 8455 AN XY: 74214

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0789

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.129

Alfa AF: 0.117 Hom.: 1471

Bravo AF: 0.110

Asia WGS AF: 0.125 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.24
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12984174; hg19: chr19-18132540;