chr5-58544912-T-C

Variant names:

• chr5-58544912-T-C
• rs10514852
• ENST00000504333.1:n.363+1180A>G

Variant summary

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

The ENST00000504333.1(LINC02108):​n.363+1180A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 152,288 control chromosomes in the GnomAD database, including 368 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 0.056 (368 hom., cov: 33)
• Consequence: LINC02108 ENST00000504333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 4 publications found

Genes affected

LINC02108 (HGNC:52963): (long intergenic non-protein coding RNA 2108)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504333.1. 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
	LINC02108	NR_109904.1		n.363+1180A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02108	ENST00000504333.1	TSL:1	n.363+1180A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8591 AN: 152170 Hom.: 363 Cov.: 33

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0479

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0839

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0565 AC: 8602 AN: 152288 Hom.: 368 Cov.: 33 AF XY: 0.0590 AC XY: 4396 AN XY: 74454

African (AFR) AF: 0.0135 AC: 560 AN: 41586

American (AMR) AF: 0.0478 AC: 731 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3470

East Asian (EAS) AF: 0.0841 AC: 436 AN: 5186

South Asian (SAS) AF: 0.126 AC: 608 AN: 4824

European-Finnish (FIN) AF: 0.102 AC: 1081 AN: 10598

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0691 AC: 4697 AN: 68018

Other (OTH) AF: 0.0569 AC: 120 AN: 2110

Alfa AF: 0.0651 Hom.: 256

Bravo AF: 0.0483

Asia WGS AF: 0.128 AC: 443 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.65
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10514852; hg19: chr5-57840739;