13-42395646-A-G

Position:

• chr13-42395646-A-G

Variant summary

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

The ENST00000637462.1(LINC02341):​n.711+1043A>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 0.0631 in 152,302 control chromosomes in the GnomAD database, including 335 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 0.063 (335 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

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=-0.82).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02341	ENST00000637462.1	n.711+1043A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0632 AC: 9612 AN: 152184 Hom.: 334 Cov.: 33

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0519

Gnomad OTH AF: 0.0573

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

GnomAD4 genome AF: 0.0631 AC: 9612 AN: 152302 Hom.: 335 Cov.: 33 AF XY: 0.0682 AC XY: 5078 AN XY: 74466

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0519

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0555 Hom.: 334

Bravo AF: 0.0547

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507508; hg19: chr13-42969782;