5-158377449-C-T

Position:

• chr5-158377449-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.129-7839G>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 0.304 in 151,980 control chromosomes in the GnomAD database, including 7,553 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 0.30 (7553 hom., cov: 32)
• Consequence: LINC02227 NR_109888.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02227	NR_109888.1	n.129-7839G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02227	ENST00000619068.1	n.129-7839G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46208 AN: 151862 Hom.: 7552 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.304 AC: 46222 AN: 151980 Hom.: 7553 Cov.: 32 AF XY: 0.303 AC XY: 22541 AN XY: 74282

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.341

Alfa AF: 0.353 Hom.: 12325

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9313772; hg19: chr5-157804457;