chr2-113969039-C-T

Variant names:

• chr2-113969039-C-T
• rs10496455

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 0.116 in 152,120 control chromosomes in the GnomAD database, including 1,615 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 0.12 (1615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• 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 (EAS) allele frequency at 95% confidence interval = 0.349 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: 0.116 AC: 17669 AN: 152002 Hom.: 1608 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.116 AC: 17700 AN: 152120 Hom.: 1615 Cov.: 32 AF XY: 0.117 AC XY: 8686 AN XY: 74360

African (AFR) AF: 0.212 AC: 8782 AN: 41440

American (AMR) AF: 0.104 AC: 1594 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1874 AN: 5166

South Asian (SAS) AF: 0.189 AC: 913 AN: 4820

European-Finnish (FIN) AF: 0.0521 AC: 552 AN: 10588

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0531 AC: 3609 AN: 68024

Other (OTH) AF: 0.0985 AC: 208 AN: 2112

Alfa AF: 0.0779 Hom.: 2276

Bravo AF: 0.125

Asia WGS AF: 0.280 AC: 972 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	1.9
DANN	Benign	0.48
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs10496455; hg19: chr2-114726616;