ENST00000422558.1:n.475+63285G>T

Variant names:

• chr2-34447854-G-T
• rs10495822
• ENST00000422558.1:n.475+63285G>T

Variant summary

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

The ENST00000422558.1(LINC01320):​n.475+63285G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,064 control chromosomes in the GnomAD database, including 6,839 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 0.27 (6839 hom., cov: 32)
• Consequence: LINC01320 ENST00000422558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422558.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01320	ENST00000422558.1	TSL:4	n.475+63285G>T		intron	N/A
	LINC01320	ENST00000650021.1		n.219+63285G>T		intron	N/A
	LINC01320	ENST00000654103.1		n.532-28710G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41082 AN: 151946 Hom.: 6838 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.270 AC: 41085 AN: 152064 Hom.: 6839 Cov.: 32 AF XY: 0.269 AC XY: 19993 AN XY: 74322

African (AFR) AF: 0.0992 AC: 4119 AN: 41532

American (AMR) AF: 0.328 AC: 4999 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3468

East Asian (EAS) AF: 0.0273 AC: 141 AN: 5174

South Asian (SAS) AF: 0.181 AC: 874 AN: 4818

European-Finnish (FIN) AF: 0.386 AC: 4074 AN: 10558

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24427 AN: 67962

Other (OTH) AF: 0.316 AC: 665 AN: 2106

Alfa AF: 0.331 Hom.: 36467

Bravo AF: 0.263

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.71
DANN	Benign	0.50
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs10495822; hg19: chr2-34672921;