ENST00000650021.1:n.167-20445C>A

Variant names:

• chr2-34364072-C-A
• rs2887987
• ENST00000650021.1:n.167-20445C>A

Variant summary

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

The ENST00000650021.1(LINC01320):​n.167-20445C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,966 control chromosomes in the GnomAD database, including 33,435 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 0.66 (33435 hom., cov: 33)
• Consequence: LINC01320 ENST00000650021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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	ENST00000650021.1	n.167-20445C>A		intron_variant	Intron 3 of 6
LINC01320	ENST00000835701.1	n.105-20445C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99786 AN: 151848 Hom.: 33420 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.657 AC: 99847 AN: 151966 Hom.: 33435 Cov.: 33 AF XY: 0.666 AC XY: 49427 AN XY: 74252

African (AFR) AF: 0.567 AC: 23517 AN: 41446

American (AMR) AF: 0.726 AC: 11066 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2250 AN: 3468

East Asian (EAS) AF: 0.944 AC: 4868 AN: 5156

South Asian (SAS) AF: 0.698 AC: 3373 AN: 4830

European-Finnish (FIN) AF: 0.750 AC: 7908 AN: 10544

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.661 AC: 44942 AN: 67966

Other (OTH) AF: 0.612 AC: 1290 AN: 2108

Alfa AF: 0.601 Hom.: 2169

Bravo AF: 0.650

Asia WGS AF: 0.772 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.58
DANN	Benign	0.39
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2887987; hg19: chr2-34589139;