ENST00000701178.1:n.95-17116T>A

Variant names:

• chr14-102573750-T-A
• rs11628318
• ENST00000701178.1:n.95-17116T>A

Variant summary

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

The ENST00000701178.1(LINC02323):​n.95-17116T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,958 control chromosomes in the GnomAD database, including 33,602 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 0.65 (33602 hom., cov: 30)
• Consequence: LINC02323 ENST00000701178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 14 publications found

Genes affected

LINC02323 (HGNC:53242): (long intergenic non-protein coding RNA 2323)

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 (NFE) allele frequency at 95% confidence interval = 0.744 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
LINC02323	ENST00000701178.1	n.95-17116T>A		intron_variant	Intron 1 of 1
LINC02323	ENST00000716869.1	n.504-15714T>A		intron_variant	Intron 2 of 3
LINC02323	ENST00000716870.1	n.436-6337T>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99128 AN: 151840 Hom.: 33600 Cov.: 30

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.652 AC: 99152 AN: 151958 Hom.: 33602 Cov.: 30 AF XY: 0.653 AC XY: 48462 AN XY: 74264

African (AFR) AF: 0.470 AC: 19471 AN: 41424

American (AMR) AF: 0.670 AC: 10211 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2903 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2768 AN: 5158

South Asian (SAS) AF: 0.728 AC: 3513 AN: 4824

European-Finnish (FIN) AF: 0.672 AC: 7092 AN: 10560

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50950 AN: 67966

Other (OTH) AF: 0.682 AC: 1437 AN: 2106

Alfa AF: 0.727 Hom.: 20092

Bravo AF: 0.639

Asia WGS AF: 0.634 AC: 2208 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	2.6
DANN	Benign	0.48
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs11628318; hg19: chr14-103040087;