rs7326018

Variant names:

• chr13-89713668-A-T
• rs7326018
• ENST00000659314.1:n.359-103583A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000659314.1(LINC02336):​n.359-103583A>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02336	ENST00000659314.1	n.359-103583A>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.533 AC: 22104 AN: 41446

American (AMR) AF: 0.393 AC: 6000 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1902 AN: 3470

East Asian (EAS) AF: 0.172 AC: 886 AN: 5154

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4820

European-Finnish (FIN) AF: 0.363 AC: 3841 AN: 10574

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.399 AC: 27097 AN: 67926

Other (OTH) AF: 0.435 AC: 918 AN: 2112

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
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs7326018; hg19: chr13-90365922;