rs4901869

Variant names:

• chr14-58867410-A-G
• rs4901869
• ENST00000553762.2:n.269-10199A>G

Variant summary

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

The ENST00000555378.5(LINC01500):​n.269-26733A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,888 control chromosomes in the GnomAD database, including 9,369 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 0.34 (9369 hom., cov: 30)
• Consequence: LINC01500 ENST00000555378.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01500	NR_110547.1	n.269-26733A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01500	ENST00000553762.2	n.269-10199A>G		intron_variant	Intron 1 of 8	5
LINC01500	ENST00000555378.5	n.269-26733A>G		intron_variant	Intron 1 of 4	3
LINC01500	ENST00000556815.6	n.295-26733A>G		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50991 AN: 151768 Hom.: 9367 Cov.: 30

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.336 AC: 51004 AN: 151888 Hom.: 9369 Cov.: 30 AF XY: 0.336 AC XY: 24946 AN XY: 74192

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0351

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.338

Alfa AF: 0.365 Hom.: 12341

Bravo AF: 0.322

Asia WGS AF: 0.125 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4901869; hg19: chr14-59334128;