rs13403149

Variant names:

• chr2-2839536-G-A
• rs13403149
• ENST00000663497.1:n.730+247C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-2839536-G-A
• chr2-2839536-G-C
• chr2-2839536-G-T

Variant summary

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

The ENST00000663497.1(ENSG00000237720):​n.730+247C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,140 control chromosomes in the GnomAD database, including 8,879 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 0.33 (8879 hom., cov: 33)
• Consequence: ENSG00000237720 ENST00000663497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 0 publications found

Genes affected

ENSG00000237720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373390	NR_187835.1	n.1089+247C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237720	ENST00000663497.1	n.730+247C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49834 AN: 152020 Hom.: 8865 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.328 AC: 49878 AN: 152140 Hom.: 8879 Cov.: 33 AF XY: 0.329 AC XY: 24442 AN XY: 74346

African (AFR) AF: 0.194 AC: 8069 AN: 41528

American (AMR) AF: 0.337 AC: 5152 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1608 AN: 3472

East Asian (EAS) AF: 0.403 AC: 2081 AN: 5160

South Asian (SAS) AF: 0.492 AC: 2373 AN: 4824

European-Finnish (FIN) AF: 0.334 AC: 3529 AN: 10574

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25962 AN: 67966

Other (OTH) AF: 0.361 AC: 764 AN: 2114

Alfa AF: 0.374 Hom.: 46722

Bravo AF: 0.323

Asia WGS AF: 0.459 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0090
DANN	Benign	0.59
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs13403149; hg19: chr2-2843308;