13-42371327-A-G

Position:

• chr13-42371327-A-G

Variant summary

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

The ENST00000637462.1(LINC02341):​n.230-12930A>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 0.265 in 152,064 control chromosomes in the GnomAD database, including 5,522 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 0.27 (5522 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866

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=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 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.230-12930A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40327 AN: 151944 Hom.: 5512 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.265 AC: 40351 AN: 152064 Hom.: 5522 Cov.: 32 AF XY: 0.267 AC XY: 19842 AN XY: 74334

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.268

Alfa AF: 0.249 Hom.: 6611

Bravo AF: 0.260

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.4
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7992970; hg19: chr13-42945463;