rs7141336

Variant names:

• chr14-90819884-A-G
• rs7141336
• ENST00000659138.3:n.*158T>C

Variant summary

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

The ENST00000659138.3(LINC02321):​n.*158T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,016 control chromosomes in the GnomAD database, including 8,384 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 0.33 (8384 hom., cov: 32)
• Consequence: LINC02321 ENST00000659138.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 4 publications found

Genes affected

LINC02321 (HGNC:53240): (long intergenic non-protein coding RNA 2321)

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 = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02321	NR_184259.1	n.*189T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02321	ENST00000659138.3	n.*158T>C		downstream_gene_variant
LINC02321	ENST00000825139.1	n.*176T>C		downstream_gene_variant
LINC02321	ENST00000825140.1	n.*180T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49477 AN: 151896 Hom.: 8373 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.326 AC: 49525 AN: 152016 Hom.: 8384 Cov.: 32 AF XY: 0.326 AC XY: 24222 AN XY: 74292

African (AFR) AF: 0.300 AC: 12421 AN: 41472

American (AMR) AF: 0.327 AC: 5003 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1104 AN: 3470

East Asian (EAS) AF: 0.130 AC: 670 AN: 5150

South Asian (SAS) AF: 0.216 AC: 1040 AN: 4818

European-Finnish (FIN) AF: 0.417 AC: 4402 AN: 10556

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23955 AN: 67958

Other (OTH) AF: 0.298 AC: 628 AN: 2108

Alfa AF: 0.340 Hom.: 1371

Bravo AF: 0.320

Asia WGS AF: 0.191 AC: 664 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	0.084
DANN	Benign	0.22
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7141336; hg19: chr14-91286228;