rs238270

Variant names:

• chr13-42358789-G-A
• rs238270
• ENST00000637462.1:n.229+16187G>A

Variant summary

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

The ENST00000637462.1(LINC02341):​n.229+16187G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,874 control chromosomes in the GnomAD database, including 12,840 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 0.40 (12840 hom., cov: 31)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 11 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 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.229+16187G>A		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61191 AN: 151756 Hom.: 12826 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.403 AC: 61248 AN: 151874 Hom.: 12840 Cov.: 31 AF XY: 0.407 AC XY: 30208 AN XY: 74228

African (AFR) AF: 0.437 AC: 18079 AN: 41368

American (AMR) AF: 0.458 AC: 6995 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1946 AN: 3466

East Asian (EAS) AF: 0.653 AC: 3371 AN: 5162

South Asian (SAS) AF: 0.451 AC: 2167 AN: 4804

European-Finnish (FIN) AF: 0.297 AC: 3135 AN: 10542

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24218 AN: 67944

Other (OTH) AF: 0.443 AC: 934 AN: 2110

Alfa AF: 0.386 Hom.: 47181

Bravo AF: 0.419

Asia WGS AF: 0.520 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.58
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs238270; hg19: chr13-42932925;