rs13153459

Positions:

• chr5-44515833-A-C
• chr5-44515833-A-T

Variant summary

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

The ENST00000671607.1(LINC02224):​n.109-11361T>G 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 0.237 in 151,790 control chromosomes in the GnomAD database, including 4,799 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 0.24 (4799 hom., cov: 31)
• Consequence: LINC02224 ENST00000671607.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

Genes affected

LINC02224 (HGNC:53093): (long intergenic non-protein coding RNA 2224)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02224	ENST00000671607.1	n.109-11361T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36003 AN: 151672 Hom.: 4786 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.237 AC: 36035 AN: 151790 Hom.: 4799 Cov.: 31 AF XY: 0.236 AC XY: 17536 AN XY: 74182

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.228

Alfa AF: 0.189 Hom.: 2123

Bravo AF: 0.247

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13153459; hg19: chr5-44515935;