rs12777679

Positions:

• chr10-87853562-T-C

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 0.184 in 151,160 control chromosomes in the GnomAD database, including 2,763 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 0.18 (2763 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.183 AC: 27709 AN: 151042 Hom.: 2742 Cov.: 28

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.184 AC: 27775 AN: 151160 Hom.: 2763 Cov.: 28 AF XY: 0.185 AC XY: 13664 AN XY: 73834

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.203

Alfa AF: 0.185 Hom.: 337

Bravo AF: 0.186

Asia WGS AF: 0.291 AC: 1012 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.053
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12777679; hg19: chr10-89613319;