rs10483709

Variant names:

• chr14-58986423-A-G
• rs10483709
• ENST00000553762.2:n.973-22608A>G

Variant summary

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

The ENST00000553762.2(LINC01500):​n.973-22608A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0845 in 152,230 control chromosomes in the GnomAD database, including 628 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 0.085 (628 hom., cov: 32)
• Consequence: LINC01500 ENST00000553762.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543
• Publications: 1 publications found

Genes affected

LINC01500 (HGNC:51166): (long intergenic non-protein coding RNA 1500)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01500	NR_110547.1	n.567-22608A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01500	ENST00000553762.2	n.973-22608A>G		intron_variant	Intron 7 of 8	5
LINC01500	ENST00000555378.5	n.567-22608A>G		intron_variant	Intron 4 of 4	3
LINC01500	ENST00000556026.1	n.247-22611A>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12864 AN: 152112 Hom.: 629 Cov.: 32

Gnomad AFR AF: 0.0639

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0508

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0845 AC: 12864 AN: 152230 Hom.: 628 Cov.: 32 AF XY: 0.0808 AC XY: 6013 AN XY: 74420

African (AFR) AF: 0.0639 AC: 2656 AN: 41534

American (AMR) AF: 0.0781 AC: 1194 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 341 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.0410 AC: 198 AN: 4826

European-Finnish (FIN) AF: 0.0508 AC: 538 AN: 10600

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7674 AN: 68018

Other (OTH) AF: 0.0885 AC: 187 AN: 2112

Alfa AF: 0.103 Hom.: 1627

Bravo AF: 0.0852

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.70
PhyloP100		0.54
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10483709; hg19: chr14-59453141;