12-73719248-A-G

Position:

• chr12-73719248-A-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 0.575 in 151,760 control chromosomes in the GnomAD database, including 25,411 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 0.57 (25411 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 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: 0.575 AC: 87195 AN: 151644 Hom.: 25404 Cov.: 31

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.575 AC: 87237 AN: 151760 Hom.: 25411 Cov.: 31 AF XY: 0.577 AC XY: 42771 AN XY: 74176

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.598

Alfa AF: 0.589 Hom.: 53141

Bravo AF: 0.565

Asia WGS AF: 0.648 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7299914; hg19: chr12-74113028;