rs1493762

Variant names:

• chr12-91686138-T-G
• rs1493762

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 0.195 in 151,970 control chromosomes in the GnomAD database, including 3,063 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 0.19 (3063 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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: 0.195 AC: 29569 AN: 151852 Hom.: 3062 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0868

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.195 AC: 29574 AN: 151970 Hom.: 3063 Cov.: 31 AF XY: 0.190 AC XY: 14088 AN XY: 74304

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0866

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.198

Alfa AF: 0.179 Hom.: 1152

Bravo AF: 0.204

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1493762; hg19: chr12-92079915;