rs13149020

Variant names:

• chr4-27192449-C-A
• rs13149020
• ENST00000829727.1:n.109+15197C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-27192449-C-A
• chr4-27192449-C-T

Variant summary

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

The ENST00000829727.1(LINC02261):​n.109+15197C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,626 control chromosomes in the GnomAD database, including 7,865 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 0.30 (7865 hom., cov: 32)
• Consequence: LINC02261 ENST00000829727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 6 publications found

Genes affected

LINC02261 (HGNC:53173): (long intergenic non-protein coding RNA 2261)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 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
LINC02261	ENST00000829727.1	n.109+15197C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46168 AN: 151514 Hom.: 7866 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.304 AC: 46156 AN: 151626 Hom.: 7865 Cov.: 32 AF XY: 0.298 AC XY: 22055 AN XY: 74084

African (AFR) AF: 0.184 AC: 7613 AN: 41394

American (AMR) AF: 0.265 AC: 4020 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3470

East Asian (EAS) AF: 0.0679 AC: 339 AN: 4994

South Asian (SAS) AF: 0.216 AC: 1039 AN: 4800

European-Finnish (FIN) AF: 0.382 AC: 4043 AN: 10570

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26882 AN: 67906

Other (OTH) AF: 0.314 AC: 661 AN: 2102

Alfa AF: 0.344 Hom.: 15592

Bravo AF: 0.292

Asia WGS AF: 0.136 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs13149020; hg19: chr4-27194071;