rs13002041

Variant names:

• chr2-57745699-C-A
• rs13002041
• ENST00000811253.1:n.148+36594G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-57745699-C-A
• chr2-57745699-C-G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000811253.1(ENSG00000285755):​n.148+36594G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,818 control chromosomes in the GnomAD database, including 26,973 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 0.59 (26973 hom., cov: 32)
• Consequence: ENSG00000285755 ENST00000811253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16
• Publications: 5 publications found

Genes affected

ENSG00000285755 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 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
ENSG00000285755	ENST00000811253.1	n.148+36594G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90264 AN: 151700 Hom.: 26956 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.595 AC: 90325 AN: 151818 Hom.: 26973 Cov.: 32 AF XY: 0.594 AC XY: 44045 AN XY: 74178

African (AFR) AF: 0.520 AC: 21525 AN: 41410

American (AMR) AF: 0.582 AC: 8872 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2251 AN: 3466

East Asian (EAS) AF: 0.619 AC: 3188 AN: 5154

South Asian (SAS) AF: 0.563 AC: 2705 AN: 4808

European-Finnish (FIN) AF: 0.650 AC: 6848 AN: 10532

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42797 AN: 67894

Other (OTH) AF: 0.601 AC: 1270 AN: 2114

Alfa AF: 0.588 Hom.: 9006

Bravo AF: 0.586

Asia WGS AF: 0.590 AC: 2051 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	22
DANN	Benign	0.65
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs13002041; hg19: chr2-57972834;