rs238252

chr13-42341518-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637462.1(LINC02341):n.108-963C>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02341	ENST00000637462.1	n.108-963C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.0930

Gnomad4 ASJ AF: 0.0884

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0691

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.149

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs238252; hg19: chr13-42915654;