13-89713668-A-T

Position:

• chr13-89713668-A-T

Variant summary

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

The ENST00000659314.1(LINC02336):​n.359-103583A>T 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 0.427 in 151,974 control chromosomes in the GnomAD database, including 14,443 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 0.43 (14443 hom., cov: 32)
• Consequence: LINC02336 ENST00000659314.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

Genes affected

LINC02336 (HGNC:53256): (long intergenic non-protein coding RNA 2336)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 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
LINC02336	ENST00000659314.1	n.359-103583A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64869 AN: 151856 Hom.: 14425 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.427 AC: 64925 AN: 151974 Hom.: 14443 Cov.: 32 AF XY: 0.422 AC XY: 31333 AN XY: 74292

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.435

Alfa AF: 0.422 Hom.: 1714

Bravo AF: 0.432

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	13
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7326018; hg19: chr13-90365922;