rs13029625

Variant names:

• chr2-137868524-G-A
• rs13029625
• ENST00000757541.1:n.150+2139C>T

Variant summary

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

The ENST00000757541.1(ENSG00000298715):​n.150+2139C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,144 control chromosomes in the GnomAD database, including 12,055 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 0.39 (12055 hom., cov: 31)
• Consequence: ENSG00000298715 ENST00000757541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 4 publications found

Genes affected

ENSG00000298715 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 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
ENSG00000298715	ENST00000757541.1	n.150+2139C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58507 AN: 151024 Hom.: 12060 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.387 AC: 58491 AN: 151144 Hom.: 12055 Cov.: 31 AF XY: 0.391 AC XY: 28869 AN XY: 73796

African (AFR) AF: 0.256 AC: 10574 AN: 41352

American (AMR) AF: 0.373 AC: 5636 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2023 AN: 3448

East Asian (EAS) AF: 0.652 AC: 3331 AN: 5108

South Asian (SAS) AF: 0.552 AC: 2652 AN: 4800

European-Finnish (FIN) AF: 0.373 AC: 3927 AN: 10532

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 28941 AN: 67484

Other (OTH) AF: 0.433 AC: 909 AN: 2100

Alfa AF: 0.399 Hom.: 5496

Bravo AF: 0.377

Asia WGS AF: 0.540 AC: 1874 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs13029625; hg19: chr2-138626094;