rs12465811

Variant names:

• chr2-34398729-T-G
• rs12465811
• ENST00000422558.1:n.475+14160T>G

Variant summary

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

The ENST00000422558.1(LINC01320):​n.475+14160T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,748 control chromosomes in the GnomAD database, including 31,365 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 0.64 (31365 hom., cov: 30)
• Consequence: LINC01320 ENST00000422558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.735 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
LINC01320	ENST00000422558.1	n.475+14160T>G		intron_variant	Intron 2 of 2	4
LINC01320	ENST00000650021.1	n.219+14160T>G		intron_variant	Intron 4 of 6
LINC01320	ENST00000654103.1	n.384-343T>G		intron_variant	Intron 2 of 5
LINC01320	ENST00000835701.1	n.157+14160T>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97457 AN: 151630 Hom.: 31338 Cov.: 30

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.643 AC: 97540 AN: 151748 Hom.: 31365 Cov.: 30 AF XY: 0.645 AC XY: 47775 AN XY: 74108

African (AFR) AF: 0.690 AC: 28524 AN: 41362

American (AMR) AF: 0.598 AC: 9116 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2181 AN: 3468

East Asian (EAS) AF: 0.644 AC: 3310 AN: 5142

South Asian (SAS) AF: 0.755 AC: 3638 AN: 4816

European-Finnish (FIN) AF: 0.604 AC: 6337 AN: 10484

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42302 AN: 67918

Other (OTH) AF: 0.644 AC: 1354 AN: 2104

Alfa AF: 0.632 Hom.: 5170

Bravo AF: 0.640

Asia WGS AF: 0.687 AC: 2387 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.47
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs12465811; hg19: chr2-34623796;