rs12972892

chr19-45479115-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 0.0765 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;