2-113141212-C-G

Variant names:

• chr2-113141212-C-G
• rs1374281

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 0.352 in 148,950 control chromosomes in the GnomAD database, including 9,819 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 0.35 (9819 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 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: 0.352 AC: 52459 AN: 148862 Hom.: 9806 Cov.: 28

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.352 AC: 52485 AN: 148950 Hom.: 9819 Cov.: 28 AF XY: 0.348 AC XY: 25190 AN XY: 72348

African (AFR) AF: 0.301 AC: 12173 AN: 40438

American (AMR) AF: 0.289 AC: 4315 AN: 14914

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1700 AN: 3454

East Asian (EAS) AF: 0.0911 AC: 461 AN: 5058

South Asian (SAS) AF: 0.481 AC: 2279 AN: 4736

European-Finnish (FIN) AF: 0.311 AC: 2957 AN: 9508

Middle Eastern (MID) AF: 0.476 AC: 137 AN: 288

European-Non Finnish (NFE) AF: 0.405 AC: 27406 AN: 67588

Other (OTH) AF: 0.382 AC: 788 AN: 2064

Alfa AF: 0.163 Hom.: 261

Bravo AF: 0.344

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.67
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs1374281; hg19: chr2-113898789;