rs13020820

Variant names:

• chr2-33755461-G-T
• rs13020820
• ENST00000366209.6:n.68+48508G>T

Variant summary

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

The ENST00000366209.6(LINC01320):​n.68+48508G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,160 control chromosomes in the GnomAD database, including 7,779 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 0.28 (7779 hom., cov: 33)
• Consequence: LINC01320 ENST00000366209.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 2 publications found

Genes affected

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

LINC01317 (HGNC:50523): (long intergenic non-protein coding RNA 1317)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.68+48508G>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.68+48508G>T		intron_variant	Intron 1 of 5	5
LINC01320	ENST00000442026.1	n.46+48508G>T		intron_variant	Intron 1 of 6	3
LINC01320	ENST00000671333.1	n.69+27827G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43329 AN: 152042 Hom.: 7780 Cov.: 33

Gnomad AFR AF: 0.0734

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.285 AC: 43321 AN: 152160 Hom.: 7779 Cov.: 33 AF XY: 0.281 AC XY: 20915 AN XY: 74390

African (AFR) AF: 0.0732 AC: 3041 AN: 41542

American (AMR) AF: 0.247 AC: 3771 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3466

East Asian (EAS) AF: 0.239 AC: 1238 AN: 5174

South Asian (SAS) AF: 0.245 AC: 1182 AN: 4826

European-Finnish (FIN) AF: 0.384 AC: 4059 AN: 10560

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.405 AC: 27523 AN: 67988

Other (OTH) AF: 0.322 AC: 680 AN: 2112

Alfa AF: 0.318 Hom.: 1576

Bravo AF: 0.265

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.72
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs13020820; hg19: chr2-33980528;