rs12763012

Variant names:

• chr10-79881442-T-C
• rs12763012

Your query was ambiguous. Multiple possible variants found:

• chr10-79881442-T-C
• chr10-79881442-T-G

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 0.114 in 152,234 control chromosomes in the GnomAD database, including 1,126 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 0.11 (1126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 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: 0.114 AC: 17289 AN: 152116 Hom.: 1113 Cov.: 32

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.114 AC: 17336 AN: 152234 Hom.: 1126 Cov.: 32 AF XY: 0.117 AC XY: 8687 AN XY: 74422

African (AFR) AF: 0.0890 AC: 3700 AN: 41562

American (AMR) AF: 0.203 AC: 3103 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3468

East Asian (EAS) AF: 0.0177 AC: 92 AN: 5186

South Asian (SAS) AF: 0.235 AC: 1133 AN: 4822

European-Finnish (FIN) AF: 0.0968 AC: 1027 AN: 10608

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7609 AN: 67986

Other (OTH) AF: 0.129 AC: 272 AN: 2114

Alfa AF: 0.102 Hom.: 339

Bravo AF: 0.118

Asia WGS AF: 0.145 AC: 505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.71
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs12763012; hg19: chr10-81641198;