ENST00000554773.2:n.152-4186C>T

Variant names:

• chr14-60319006-C-T
• rs2350890
• ENST00000554773.2:n.152-4186C>T

Variant summary

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

The ENST00000554773.2(LINC02322):​n.152-4186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,856 control chromosomes in the GnomAD database, including 18,839 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 0.49 (18839 hom., cov: 30)
• Consequence: LINC02322 ENST00000554773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 3 publications found

Genes affected

LINC02322 (HGNC:53241): (long intergenic non-protein coding RNA 2322)

ENSG00000296765 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.616 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
LINC02322	ENST00000554773.2	n.152-4186C>T		intron_variant	Intron 1 of 2	2
ENSG00000296765	ENST00000741815.1	n.267-769G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74916 AN: 151738 Hom.: 18830 Cov.: 30

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.494 AC: 74964 AN: 151856 Hom.: 18839 Cov.: 30 AF XY: 0.495 AC XY: 36760 AN XY: 74204

African (AFR) AF: 0.422 AC: 17476 AN: 41374

American (AMR) AF: 0.515 AC: 7863 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2159 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2532 AN: 5160

South Asian (SAS) AF: 0.634 AC: 3056 AN: 4818

European-Finnish (FIN) AF: 0.520 AC: 5471 AN: 10512

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.512 AC: 34762 AN: 67934

Other (OTH) AF: 0.516 AC: 1087 AN: 2108

Alfa AF: 0.512 Hom.: 35854

Bravo AF: 0.489

Asia WGS AF: 0.549 AC: 1909 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	0.74
DANN	Benign	0.32
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2350890; hg19: chr14-60785724;