rs1493762

Variant names:

• chr12-91686138-T-G
• rs1493762

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.259 AC: 10736 AN: 41426

American (AMR) AF: 0.215 AC: 3275 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3466

East Asian (EAS) AF: 0.0866 AC: 448 AN: 5174

South Asian (SAS) AF: 0.122 AC: 589 AN: 4818

European-Finnish (FIN) AF: 0.127 AC: 1346 AN: 10578

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12075 AN: 67934

Other (OTH) AF: 0.198 AC: 417 AN: 2110

Alfa AF: 0.180 Hom.: 1290

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1493762; hg19: chr12-92079915;