5-29040014-T-G

Variant names:

• chr5-29040014-T-G
• rs488884
• ENST00000658190.1:n.819-122402T>G

Variant summary

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

The ENST00000658190.1(LINC02109):​n.819-122402T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,754 control chromosomes in the GnomAD database, including 23,973 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 0.56 (23973 hom., cov: 31)
• Consequence: LINC02109 ENST00000658190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

LINC02109 (HGNC:52964): (long intergenic non-protein coding RNA 2109)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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
LINC02109	ENST00000658190.1	n.819-122402T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84214 AN: 151636 Hom.: 23943 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.556 AC: 84308 AN: 151754 Hom.: 23973 Cov.: 31 AF XY: 0.560 AC XY: 41526 AN XY: 74136

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.540

Alfa AF: 0.514 Hom.: 2451

Bravo AF: 0.565

Asia WGS AF: 0.670 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs488884; hg19: chr5-29040121;