rs10859725

Variant names:

• chr12-94550096-T-C
• rs10859725

Your query was ambiguous. Multiple possible variants found:

• chr12-94550096-T-C
• chr12-94550096-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 0.238 in 152,072 control chromosomes in the GnomAD database, including 5,055 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 0.24 (5055 hom., cov: 33)
• Consequence: SUCLG2P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• Publications: 5 publications found

Genes affected

SUCLG2P2 (HGNC:43997): (SUCLG2 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36194 AN: 151954 Hom.: 5055 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.238 AC: 36219 AN: 152072 Hom.: 5055 Cov.: 33 AF XY: 0.235 AC XY: 17468 AN XY: 74338

African (AFR) AF: 0.380 AC: 15755 AN: 41430

American (AMR) AF: 0.205 AC: 3136 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1752 AN: 5172

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4818

European-Finnish (FIN) AF: 0.130 AC: 1372 AN: 10592

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11817 AN: 68002

Other (OTH) AF: 0.208 AC: 440 AN: 2116

Alfa AF: 0.202 Hom.: 9645

Bravo AF: 0.255

Asia WGS AF: 0.221 AC: 770 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10859725; hg19: chr12-94943872; COSMIC: COSV56217631;