ENST00000637462.1:n.230-1772C>T

Variant names:

• chr13-42382485-C-T
• rs17638544
• ENST00000637462.1:n.230-1772C>T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.230-1772C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0638 in 152,042 control chromosomes in the GnomAD database, including 334 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 0.064 (334 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 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.230-1772C>T		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9702 AN: 151924 Hom.: 333 Cov.: 32

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0532

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0638 AC: 9703 AN: 152042 Hom.: 334 Cov.: 32 AF XY: 0.0691 AC XY: 5131 AN XY: 74294

Gnomad4 AFR AF: 0.0604

Gnomad4 AMR AF: 0.0340

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0532

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0565 Hom.: 347

Bravo AF: 0.0555

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
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: rs17638544; hg19: chr13-42956621;