rs2149954

chr5-158393594-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109888.1(LINC02227):n.128+16052G>A variant causes a intron, non coding transcript 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 NR_109888.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02227	NR_109888.1	n.128+16052G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02227	ENST00000619068.1	n.128+16052G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.399

Alfa AF: 0.357 Hom.: 1704

Bravo AF: 0.357

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.025
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2149954; hg19: chr5-157820602;