rs12972892

Variant names:

• chr19-45479115-T-G
• rs12972892

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 0.0765 in 152,176 control chromosomes in the GnomAD database, including 649 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 0.076 (649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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: 0.0765 AC: 11637 AN: 152058 Hom.: 647 Cov.: 32

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0765 AC: 11635 AN: 152176 Hom.: 649 Cov.: 32 AF XY: 0.0799 AC XY: 5941 AN XY: 74396

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0293

Gnomad4 NFE AF: 0.0753

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0646 Hom.: 59

Bravo AF: 0.0843

Asia WGS AF: 0.127 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12972892; hg19: chr19-45982373;