ENST00000422558.1:n.475+89679C>T

Variant names:

• chr2-34474248-C-T
• rs7593687
• ENST00000422558.1:n.475+89679C>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+89679C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 133,852 control chromosomes in the GnomAD database, including 1,700 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 0.076 (1700 hom., cov: 23)
• Consequence: LINC01320 ENST00000422558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 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+89679C>T		intron	N/A
	LINC01320	ENST00000650021.1		n.219+89679C>T		intron	N/A
	LINC01320	ENST00000654103.1		n.532-2316C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 10141 AN: 133740 Hom.: 1698 Cov.: 23

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.00233

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000680

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0219

Gnomad NFE AF: 0.00153

Gnomad OTH AF: 0.0600

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

GnomAD4 genome AF: 0.0758 AC: 10152 AN: 133852 Hom.: 1700 Cov.: 23 AF XY: 0.0737 AC XY: 4795 AN XY: 65074

African (AFR) AF: 0.234 AC: 9481 AN: 40436

American (AMR) AF: 0.0366 AC: 463 AN: 12656

Ashkenazi Jewish (ASJ) AF: 0.00233 AC: 7 AN: 3000

East Asian (EAS) AF: 0.00 AC: 0 AN: 5140

South Asian (SAS) AF: 0.000455 AC: 2 AN: 4398

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8308

Middle Eastern (MID) AF: 0.0236 AC: 6 AN: 254

European-Non Finnish (NFE) AF: 0.00153 AC: 88 AN: 57336

Other (OTH) AF: 0.0593 AC: 105 AN: 1772

Alfa AF: 0.0594 Hom.: 123

Asia WGS AF: 0.0110 AC: 39 AN: 3378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.96
DANN	Benign	0.75
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7593687; hg19: chr2-34699315;