rs12984174

Variant names:

• chr19-18021731-T-C
• rs12984174

Your query was ambiguous. Multiple possible variants found:

• chr19-18021731-T-C
• chr19-18021731-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;