chr5-29040014-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658190.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02109	ENST00000658190.1		n.819-122402T>G		intron	N/A

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

African (AFR) AF: 0.621 AC: 25721 AN: 41394

American (AMR) AF: 0.566 AC: 8618 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1920 AN: 3460

East Asian (EAS) AF: 0.858 AC: 4417 AN: 5148

South Asian (SAS) AF: 0.597 AC: 2869 AN: 4802

European-Finnish (FIN) AF: 0.517 AC: 5433 AN: 10518

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.494 AC: 33563 AN: 67890

Other (OTH) AF: 0.540 AC: 1143 AN: 2116

Alfa AF: 0.519 Hom.: 2613

Bravo AF: 0.565

Asia WGS AF: 0.670 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs488884; hg19: chr5-29040121;