rs10513203

Variant names:

• chr5-15207207-G-A
• rs10513203
• ENST00000511443.1:n.248-14758C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-15207207-G-A
• chr5-15207207-G-T

Variant summary

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

The ENST00000511443.1(LINC02149):​n.248-14758C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0189 in 152,258 control chromosomes in the GnomAD database, including 96 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 0.019 (96 hom., cov: 32)
• Consequence: LINC02149 ENST00000511443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 0 publications found

Genes affected

LINC02149 (HGNC:53010): (long intergenic non-protein coding RNA 2149)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02149	NR_109944.1	n.267-14758C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02149	ENST00000511443.1	n.248-14758C>T		intron_variant	Intron 2 of 2	1
LINC02149	ENST00000788346.1	n.406-14758C>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 2877 AN: 152140 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00454

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.00810

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0189 AC: 2872 AN: 152258 Hom.: 96 Cov.: 32 AF XY: 0.0193 AC XY: 1434 AN XY: 74434

African (AFR) AF: 0.00452 AC: 188 AN: 41564

American (AMR) AF: 0.0149 AC: 228 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00605 AC: 21 AN: 3472

East Asian (EAS) AF: 0.176 AC: 910 AN: 5174

South Asian (SAS) AF: 0.0289 AC: 139 AN: 4818

European-Finnish (FIN) AF: 0.00810 AC: 86 AN: 10612

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0181 AC: 1230 AN: 68014

Other (OTH) AF: 0.0104 AC: 22 AN: 2110

Alfa AF: 0.0188 Hom.: 34

Bravo AF: 0.0202

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.23
DANN	Benign	0.62
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10513203; hg19: chr5-15207316;