chr13-42440328-G-A

Position:

• chr13-42440328-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_135319.1(LINC02341):​n.336+2856G>A 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 0.175 in 152,202 control chromosomes in the GnomAD database, including 2,790 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 0.17 (2790 hom., cov: 32)
• Consequence: LINC02341 NR_135319.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02341	NR_135319.1	n.336+2856G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02341	ENST00000637462.1	n.1117+2856G>A		intron_variant, non_coding_transcript_variant		5
LINC02341	ENST00000637043.1	n.336+2856G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26587 AN: 152084 Hom.: 2782 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.175 AC: 26597 AN: 152202 Hom.: 2790 Cov.: 32 AF XY: 0.173 AC XY: 12841 AN XY: 74402

Gnomad4 AFR AF: 0.0693

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.188

Alfa AF: 0.121 Hom.: 302

Bravo AF: 0.166

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	9.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12864265; hg19: chr13-43014464;