chr13-42413358-A-G

Position:

• chr13-42413358-A-G

Variant summary

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

The ENST00000637462.1(LINC02341):​n.868+1306A>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 0.294 in 152,200 control chromosomes in the GnomAD database, including 7,259 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 0.29 (7259 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

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 (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02341	ENST00000637462.1	n.868+1306A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44713 AN: 152082 Hom.: 7250 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.294 AC: 44755 AN: 152200 Hom.: 7259 Cov.: 33 AF XY: 0.293 AC XY: 21787 AN XY: 74414

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.307

Alfa AF: 0.276 Hom.: 1038

Bravo AF: 0.318

Asia WGS AF: 0.346 AC: 1206 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11147871; hg19: chr13-42987494;