rs4513299

Variant names:

• chr2-114292241-C-G
• rs4513299

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.401 in 151,896 control chromosomes in the GnomAD database, including 12,352 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 0.40 (12352 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 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: 0.401 AC: 60930 AN: 151778 Hom.: 12342 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.401 AC: 60974 AN: 151896 Hom.: 12352 Cov.: 31 AF XY: 0.399 AC XY: 29634 AN XY: 74246

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.388

Alfa AF: 0.408 Hom.: 7007

Bravo AF: 0.398

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4513299; hg19: chr2-115049818; COSMIC: COSV60094570;