14-59010696-C-T

Variant names:

• chr14-59010696-C-T
• rs1956197
• ENST00000553762.2:n.1092+1546C>T

Variant summary

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

The ENST00000553762.2(LINC01500):​n.1092+1546C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 152,160 control chromosomes in the GnomAD database, including 56,067 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 0.86 (56067 hom., cov: 33)
• Consequence: LINC01500 ENST00000553762.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 4 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553762.2. 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
	LINC01500	NR_110547.1		n.686+1546C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01500	ENST00000553762.2	TSL:5	n.1092+1546C>T		intron	N/A
	LINC01500	ENST00000556026.1	TSL:3	n.363+1546C>T		intron	N/A
	LINC01500	ENST00000556815.6	TSL:3	n.812+1546C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130456 AN: 152042 Hom.: 56036 Cov.: 33

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.858 AC: 130544 AN: 152160 Hom.: 56067 Cov.: 33 AF XY: 0.856 AC XY: 63631 AN XY: 74366

African (AFR) AF: 0.859 AC: 35666 AN: 41512

American (AMR) AF: 0.910 AC: 13923 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3101 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4487 AN: 5178

South Asian (SAS) AF: 0.866 AC: 4170 AN: 4818

European-Finnish (FIN) AF: 0.788 AC: 8316 AN: 10548

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58035 AN: 68020

Other (OTH) AF: 0.887 AC: 1872 AN: 2110

Alfa AF: 0.859 Hom.: 27991

Bravo AF: 0.868

Asia WGS AF: 0.852 AC: 2961 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.15
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1956197; hg19: chr14-59477414;