10-112134339-C-T

Variant names:

• chr10-112134339-C-T
• rs2246253

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 0.337 in 152,084 control chromosomes in the GnomAD database, including 13,285 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 0.34 (13285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 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: 0.336 AC: 51061 AN: 151966 Hom.: 13224 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.0999

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.337 AC: 51187 AN: 152084 Hom.: 13285 Cov.: 32 AF XY: 0.335 AC XY: 24874 AN XY: 74352

African (AFR) AF: 0.727 AC: 30151 AN: 41452

American (AMR) AF: 0.272 AC: 4150 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0999 AC: 347 AN: 3472

East Asian (EAS) AF: 0.325 AC: 1679 AN: 5168

South Asian (SAS) AF: 0.251 AC: 1207 AN: 4816

European-Finnish (FIN) AF: 0.176 AC: 1866 AN: 10588

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10920 AN: 67990

Other (OTH) AF: 0.316 AC: 667 AN: 2114

Alfa AF: 0.239 Hom.: 5192

Bravo AF: 0.360

Asia WGS AF: 0.380 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.063
DANN	Benign	0.36
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs2246253; hg19: chr10-113894097;