2-34589070-T-C

Variant names:

• chr2-34589070-T-C
• rs1220213
• ENST00000422558.1:n.476-46179T>C

Variant summary

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

The ENST00000422558.1(LINC01320):​n.476-46179T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,052 control chromosomes in the GnomAD database, including 58,257 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 0.87 (58257 hom., cov: 32)
• Consequence: LINC01320 ENST00000422558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 1 publications found

Genes affected

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

ENSG00000308718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 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.476-46179T>C		intron_variant	Intron 2 of 2	4
LINC01320	ENST00000650021.1	n.220-74704T>C		intron_variant	Intron 4 of 6
LINC01320	ENST00000654103.1	n.598-8884T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132379 AN: 151934 Hom.: 58209 Cov.: 32

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.871 AC: 132485 AN: 152052 Hom.: 58257 Cov.: 32 AF XY: 0.863 AC XY: 64113 AN XY: 74306

African (AFR) AF: 0.950 AC: 39439 AN: 41536

American (AMR) AF: 0.808 AC: 12327 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3090 AN: 3472

East Asian (EAS) AF: 0.540 AC: 2781 AN: 5148

South Asian (SAS) AF: 0.701 AC: 3377 AN: 4818

European-Finnish (FIN) AF: 0.835 AC: 8807 AN: 10552

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59791 AN: 67952

Other (OTH) AF: 0.868 AC: 1834 AN: 2114

Alfa AF: 0.881 Hom.: 3628

Bravo AF: 0.877

Asia WGS AF: 0.640 AC: 2223 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1220213; hg19: chr2-34814137;