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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0890

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0177

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.0968

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.129

Alfa AF: 0.101 Hom.: 307

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12763012; hg19: chr10-81641198;