rs4513299

Variant names:

• chr2-114292241-C-G
• rs4513299
• ENST00000801755.1:n.252-58933C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000801755.1(ENSG00000304278):​n.252-58933C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000304278 ENST00000801755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 6 publications found

Genes affected

ENSG00000304278 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000304278	ENST00000801755.1	n.252-58933C>G		intron_variant	Intron 2 of 2
ENSG00000304278	ENST00000801756.1	n.289+23676C>G		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.384 AC: 15901 AN: 41394

American (AMR) AF: 0.363 AC: 5537 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1223 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1841 AN: 5138

South Asian (SAS) AF: 0.397 AC: 1912 AN: 4818

European-Finnish (FIN) AF: 0.450 AC: 4748 AN: 10548

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.419 AC: 28474 AN: 67958

Other (OTH) AF: 0.388 AC: 818 AN: 2110

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
PhyloP100		0.18

Splicing

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

Other links and lift over

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