rs12465811

Positions:

• chr2-34398729-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422558.1(LINC01320):​n.475+14160T>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01320	ENST00000422558.1	n.475+14160T>G		intron_variant, non_coding_transcript_variant		4
LINC01320	ENST00000650021.1	n.219+14160T>G		intron_variant, non_coding_transcript_variant
LINC01320	ENST00000654103.1	n.384-343T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.644

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12465811; hg19: chr2-34623796;