rs10506115

Variant names:

• chr12-33693042-G-A
• rs10506115

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 0.206 in 151,920 control chromosomes in the GnomAD database, including 4,898 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 0.21 (4898 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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: 0.206 AC: 31258 AN: 151802 Hom.: 4897 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.206 AC: 31289 AN: 151920 Hom.: 4898 Cov.: 33 AF XY: 0.216 AC XY: 16040 AN XY: 74242

African (AFR) AF: 0.290 AC: 12004 AN: 41422

American (AMR) AF: 0.244 AC: 3726 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3472

East Asian (EAS) AF: 0.800 AC: 4134 AN: 5170

South Asian (SAS) AF: 0.338 AC: 1623 AN: 4808

European-Finnish (FIN) AF: 0.165 AC: 1735 AN: 10546

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.101 AC: 6850 AN: 67948

Other (OTH) AF: 0.196 AC: 414 AN: 2108

Alfa AF: 0.152 Hom.: 924

Bravo AF: 0.214

Asia WGS AF: 0.544 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.48
DANN	Benign	0.37
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10506115; hg19: chr12-33845977;