rs238270

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.443

Alfa AF: 0.388 Hom.: 21983

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs238270; hg19: chr13-42932925;