5-158393594-C-T

Variant names:

• chr5-158393594-C-T
• rs2149954
• ENST00000619068.1:n.128+16052G>A

Variant summary

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

The ENST00000619068.1(LINC02227):​n.128+16052G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,776 control chromosomes in the GnomAD database, including 10,169 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 0.36 (10169 hom., cov: 32)
• Consequence: LINC02227 ENST00000619068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 26 publications found

Genes affected

LINC02227 (HGNC:53096): (long intergenic non-protein coding RNA 2227)

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 (SAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619068.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02227	NR_109888.1		n.128+16052G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02227	ENST00000619068.1	TSL:1	n.128+16052G>A		intron	N/A
	LINC02227	ENST00000809484.1		n.174-357G>A		intron	N/A
	LINC02227	ENST00000809485.1		n.214-23984G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55044 AN: 151658 Hom.: 10163 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.363 AC: 55081 AN: 151776 Hom.: 10169 Cov.: 32 AF XY: 0.360 AC XY: 26713 AN XY: 74168

African (AFR) AF: 0.388 AC: 16088 AN: 41414

American (AMR) AF: 0.308 AC: 4687 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3470

East Asian (EAS) AF: 0.185 AC: 951 AN: 5134

South Asian (SAS) AF: 0.401 AC: 1924 AN: 4804

European-Finnish (FIN) AF: 0.338 AC: 3562 AN: 10534

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25161 AN: 67880

Other (OTH) AF: 0.399 AC: 840 AN: 2104

Alfa AF: 0.361 Hom.: 15913

Bravo AF: 0.357

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.025
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2149954;

hg19: chr5-157820602;