5-29027515-C-T

Variant names:

• chr5-29027515-C-T
• rs16898558
• ENST00000658190.1:n.819-134901C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658190.1(LINC02109):​n.819-134901C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,054 control chromosomes in the GnomAD database, including 4,547 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 0.21 (4547 hom., cov: 32)
• Consequence: LINC02109 ENST00000658190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02109	ENST00000658190.1		n.819-134901C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32161 AN: 151934 Hom.: 4539 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.212 AC: 32196 AN: 152054 Hom.: 4547 Cov.: 32 AF XY: 0.220 AC XY: 16326 AN XY: 74316

African (AFR) AF: 0.202 AC: 8401 AN: 41494

American (AMR) AF: 0.270 AC: 4121 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3470

East Asian (EAS) AF: 0.818 AC: 4200 AN: 5132

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4818

European-Finnish (FIN) AF: 0.175 AC: 1852 AN: 10568

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10775 AN: 67980

Other (OTH) AF: 0.209 AC: 440 AN: 2110

Alfa AF: 0.192 Hom.: 523

Bravo AF: 0.221

Asia WGS AF: 0.513 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.67
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs16898558; hg19: chr5-29027622;