rs13432090

Variant names:

• chr2-33876873-T-C
• rs13432090
• ENST00000366209.6:n.134+21120T>C

Variant summary

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

The ENST00000366209.6(LINC01320):​n.134+21120T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,258 control chromosomes in the GnomAD database, including 1,985 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 0.15 (1985 hom., cov: 33)
• Consequence: LINC01320 ENST00000366209.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01317	NR_126403.1	n.134+21120T>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000366209.6	n.134+21120T>C		intron_variant	Intron 2 of 5	5
LINC01320	ENST00000442026.1	n.113-9499T>C		intron_variant	Intron 2 of 6	3
LINC01320	ENST00000667658.1	n.307-9499T>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22351 AN: 152140 Hom.: 1982 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0981

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.147 AC: 22373 AN: 152258 Hom.: 1985 Cov.: 33 AF XY: 0.147 AC XY: 10961 AN XY: 74456

African (AFR) AF: 0.167 AC: 6935 AN: 41530

American (AMR) AF: 0.116 AC: 1773 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3470

East Asian (EAS) AF: 0.432 AC: 2236 AN: 5172

South Asian (SAS) AF: 0.223 AC: 1077 AN: 4830

European-Finnish (FIN) AF: 0.0981 AC: 1041 AN: 10610

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8541 AN: 68020

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.136 Hom.: 244

Bravo AF: 0.149

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.73
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs13432090; hg19: chr2-34101940;