rs1493829

Positions:

• chr12-74590978-C-A
• chr12-74590978-C-G
• chr12-74590978-C-T

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 0.717 in 152,000 control chromosomes in the GnomAD database, including 39,560 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 0.72 (39560 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.717 AC: 108957 AN: 151882 Hom.: 39529 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.717 AC: 109041 AN: 152000 Hom.: 39560 Cov.: 32 AF XY: 0.725 AC XY: 53859 AN XY: 74328

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.716

Alfa AF: 0.619 Hom.: 1967

Bravo AF: 0.712

Asia WGS AF: 0.886 AC: 3080 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.038
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1493829; hg19: chr12-74984758;