rs10505799

Variant names:

• chr12-16293334-T-C
• rs10505799

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 0.1 in 152,150 control chromosomes in the GnomAD database, including 1,254 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 0.10 (1254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 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: 0.100 AC: 15231 AN: 152032 Hom.: 1253 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0814

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

GnomAD4 genome AF: 0.100 AC: 15243 AN: 152150 Hom.: 1254 Cov.: 32 AF XY: 0.0966 AC XY: 7187 AN XY: 74374

African (AFR) AF: 0.230 AC: 9519 AN: 41452

American (AMR) AF: 0.0696 AC: 1064 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3470

East Asian (EAS) AF: 0.0431 AC: 223 AN: 5180

South Asian (SAS) AF: 0.0232 AC: 112 AN: 4824

European-Finnish (FIN) AF: 0.0171 AC: 181 AN: 10608

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3585 AN: 68018

Other (OTH) AF: 0.0815 AC: 172 AN: 2110

Alfa AF: 0.0705 Hom.: 1803

Bravo AF: 0.111

Asia WGS AF: 0.0500 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.72
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10505799; hg19: chr12-16446268;