rs238252

Variant names:

• chr13-42341518-C-G
• rs238252
• ENST00000637462.1:n.108-963C>G

Variant summary

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

The ENST00000637462.1(LINC02341):​n.108-963C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,072 control chromosomes in the GnomAD database, including 2,416 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 0.17 (2416 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 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.108-963C>G		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25458 AN: 151954 Hom.: 2416 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.0884

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0692

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.168 AC: 25477 AN: 152072 Hom.: 2416 Cov.: 32 AF XY: 0.164 AC XY: 12176 AN XY: 74344

African (AFR) AF: 0.258 AC: 10682 AN: 41444

American (AMR) AF: 0.0930 AC: 1421 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0884 AC: 307 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5182

South Asian (SAS) AF: 0.0691 AC: 332 AN: 4806

European-Finnish (FIN) AF: 0.193 AC: 2038 AN: 10584

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10189 AN: 67994

Other (OTH) AF: 0.149 AC: 314 AN: 2106

Alfa AF: 0.170 Hom.: 299

Bravo AF: 0.163

Asia WGS AF: 0.0540 AC: 190 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.54
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs238252; hg19: chr13-42915654;