chr13-42403303-C-T

Variant names:

• chr13-42403303-C-T
• rs7994531
• ENST00000637462.1:n.712-8593C>T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.712-8593C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,734 control chromosomes in the GnomAD database, including 10,978 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 0.35 (10978 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.17
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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.712-8593C>T		intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53259 AN: 151616 Hom.: 10953 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.352 AC: 53336 AN: 151734 Hom.: 10978 Cov.: 33 AF XY: 0.350 AC XY: 25972 AN XY: 74178

African (AFR) AF: 0.540 AC: 22264 AN: 41202

American (AMR) AF: 0.406 AC: 6184 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 991 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3149 AN: 5168

South Asian (SAS) AF: 0.243 AC: 1171 AN: 4826

European-Finnish (FIN) AF: 0.192 AC: 2026 AN: 10544

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16617 AN: 67960

Other (OTH) AF: 0.349 AC: 736 AN: 2106

Alfa AF: 0.277 Hom.: 7401

Bravo AF: 0.377

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.031
DANN	Benign	0.70
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs7994531; hg19: chr13-42977439;