rs13169538

Positions:

• chr5-44569938-G-A
• chr5-44569938-G-T

Variant summary

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

The ENST00000671607.1(LINC02224):​n.109-65466C>T 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 0.0778 in 151,942 control chromosomes in the GnomAD database, including 565 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 0.078 (565 hom., cov: 32)
• Consequence: LINC02224 ENST00000671607.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02224	ENST00000671607.1	n.109-65466C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11808 AN: 151824 Hom.: 561 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0832

Gnomad EAS AF: 0.00600

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0715

Gnomad OTH AF: 0.0786

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

GnomAD4 genome AF: 0.0778 AC: 11824 AN: 151942 Hom.: 565 Cov.: 32 AF XY: 0.0761 AC XY: 5651 AN XY: 74270

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0678

Gnomad4 ASJ AF: 0.0832

Gnomad4 EAS AF: 0.00601

Gnomad4 SAS AF: 0.0211

Gnomad4 FIN AF: 0.0563

Gnomad4 NFE AF: 0.0715

Gnomad4 OTH AF: 0.0778

Alfa AF: 0.0687 Hom.: 547

Bravo AF: 0.0808

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13169538; hg19: chr5-44570040;