13-89750579-A-G

Variant names:

• chr13-89750579-A-G
• rs1327328
• ENST00000659314.1:n.359-66672A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659314.1(LINC02336):​n.359-66672A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,874 control chromosomes in the GnomAD database, including 12,888 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 0.41 (12888 hom., cov: 32)
• Consequence: LINC02336 ENST00000659314.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659314.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02336	ENST00000659314.1		n.359-66672A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62238 AN: 151756 Hom.: 12888 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.410 AC: 62272 AN: 151874 Hom.: 12888 Cov.: 32 AF XY: 0.407 AC XY: 30189 AN XY: 74200

African (AFR) AF: 0.424 AC: 17567 AN: 41438

American (AMR) AF: 0.396 AC: 6031 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1910 AN: 3460

East Asian (EAS) AF: 0.273 AC: 1404 AN: 5150

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4822

European-Finnish (FIN) AF: 0.388 AC: 4096 AN: 10556

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28124 AN: 67908

Other (OTH) AF: 0.427 AC: 898 AN: 2104

Alfa AF: 0.372 Hom.: 3455

Bravo AF: 0.409

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.9
DANN	Benign	0.75
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1327328; hg19: chr13-90402833;