rs11147871

Variant names:

• chr13-42413358-A-G
• rs11147871
• ENST00000637462.1:n.868+1306A>G

Variant summary

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

The ENST00000637462.1(LINC02341):​n.868+1306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,200 control chromosomes in the GnomAD database, including 7,259 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 0.29 (7259 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 4 publications found

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 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
LINC02341	ENST00000637462.1	n.868+1306A>G		intron_variant	Intron 5 of 7	5

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44713 AN: 152082 Hom.: 7250 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.294 AC: 44755 AN: 152200 Hom.: 7259 Cov.: 33 AF XY: 0.293 AC XY: 21787 AN XY: 74414

African (AFR) AF: 0.371 AC: 15379 AN: 41484

American (AMR) AF: 0.382 AC: 5847 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3468

East Asian (EAS) AF: 0.559 AC: 2896 AN: 5182

South Asian (SAS) AF: 0.208 AC: 1005 AN: 4826

European-Finnish (FIN) AF: 0.165 AC: 1750 AN: 10596

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.236 AC: 16080 AN: 68020

Other (OTH) AF: 0.307 AC: 650 AN: 2116

Alfa AF: 0.279 Hom.: 1095

Bravo AF: 0.318

Asia WGS AF: 0.346 AC: 1206 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.47
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11147871; hg19: chr13-42987494;