14-60322458-C-T

Variant names:

• chr14-60322458-C-T
• rs4901977
• ENST00000554773.2:n.152-734C>T

Variant summary

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

The ENST00000554773.2(LINC02322):​n.152-734C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,978 control chromosomes in the GnomAD database, including 12,629 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 0.39 (12629 hom., cov: 32)
• Consequence: LINC02322 ENST00000554773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 23 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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.152-734C>T		intron_variant	Intron 1 of 2	2
ENSG00000296765	ENST00000741815.1	n.267-4221G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58481 AN: 151860 Hom.: 12629 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.385 AC: 58516 AN: 151978 Hom.: 12629 Cov.: 32 AF XY: 0.382 AC XY: 28363 AN XY: 74276

African (AFR) AF: 0.573 AC: 23771 AN: 41456

American (AMR) AF: 0.292 AC: 4464 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1397 AN: 3466

East Asian (EAS) AF: 0.563 AC: 2914 AN: 5174

South Asian (SAS) AF: 0.316 AC: 1521 AN: 4814

European-Finnish (FIN) AF: 0.234 AC: 2466 AN: 10532

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20666 AN: 67954

Other (OTH) AF: 0.399 AC: 841 AN: 2106

Alfa AF: 0.339 Hom.: 37935

Bravo AF: 0.398

Asia WGS AF: 0.451 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.57
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs4901977; hg19: chr14-60789176;