5-158418394-C-T

Variant names:

• chr5-158418394-C-T
• rs11953630
• ENST00000809484.1:n.174-25157G>A

Variant summary

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

The ENST00000809484.1(LINC02227):​n.174-25157G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,008 control chromosomes in the GnomAD database, including 7,324 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 0.29 (7324 hom., cov: 32)
• Consequence: LINC02227 ENST00000809484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 65 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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
LINC02227	ENST00000809484.1	n.174-25157G>A		intron_variant	Intron 2 of 3
LINC02227	ENST00000809485.1	n.213+11780G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44735 AN: 151888 Hom.: 7325 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0725

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.294 AC: 44744 AN: 152008 Hom.: 7324 Cov.: 32 AF XY: 0.293 AC XY: 21759 AN XY: 74310

African (AFR) AF: 0.181 AC: 7521 AN: 41476

American (AMR) AF: 0.271 AC: 4134 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1407 AN: 3468

East Asian (EAS) AF: 0.0727 AC: 376 AN: 5172

South Asian (SAS) AF: 0.358 AC: 1725 AN: 4820

European-Finnish (FIN) AF: 0.334 AC: 3524 AN: 10562

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24977 AN: 67956

Other (OTH) AF: 0.331 AC: 697 AN: 2106

Alfa AF: 0.332 Hom.: 16883

Bravo AF: 0.279

Asia WGS AF: 0.246 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.031
DANN	Benign	0.47
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11953630; hg19: chr5-157845402;