rs13024450

Variant names:

• chr2-136257041-C-T
• rs13024450
• ENST00000837573.1:n.120+10516C>T

Variant summary

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

The ENST00000837573.1(ENSG00000308974):​n.120+10516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,094 control chromosomes in the GnomAD database, including 14,483 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 0.37 (14483 hom., cov: 32)
• Consequence: ENSG00000308974 ENST00000837573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 4 publications found

Genes affected

ENSG00000308974 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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
ENSG00000308974	ENST00000837573.1	n.120+10516C>T		intron_variant	Intron 1 of 1
ENSG00000308974	ENST00000837574.1	n.284+2897C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56130 AN: 151976 Hom.: 14487 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0278

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.369 AC: 56117 AN: 152094 Hom.: 14483 Cov.: 32 AF XY: 0.361 AC XY: 26868 AN XY: 74336

African (AFR) AF: 0.111 AC: 4601 AN: 41520

American (AMR) AF: 0.221 AC: 3380 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3472

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5176

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4810

European-Finnish (FIN) AF: 0.617 AC: 6523 AN: 10570

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38597 AN: 67966

Other (OTH) AF: 0.270 AC: 571 AN: 2114

Alfa AF: 0.460 Hom.: 5208

Bravo AF: 0.326

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs13024450; hg19: chr2-137014611;