ENST00000654440.1:n.809+11625G>C

Variant names:

• chr14-59091401-G-C
• rs1954004
• ENST00000654440.1:n.809+11625G>C

Variant summary

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

The ENST00000654440.1(LINC01500):​n.809+11625G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,178 control chromosomes in the GnomAD database, including 50,225 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 0.81 (50225 hom., cov: 31)
• Consequence: LINC01500 ENST00000654440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654440.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01500	ENST00000654440.1		n.809+11625G>C		intron	N/A
	LINC01500	ENST00000655076.1		n.913+11625G>C		intron	N/A
	LINC01500	ENST00000656663.1		n.526-3154G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123445 AN: 152060 Hom.: 50179 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.812 AC: 123553 AN: 152178 Hom.: 50225 Cov.: 31 AF XY: 0.808 AC XY: 60093 AN XY: 74384

African (AFR) AF: 0.860 AC: 35701 AN: 41522

American (AMR) AF: 0.819 AC: 12527 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2821 AN: 3472

East Asian (EAS) AF: 0.743 AC: 3845 AN: 5176

South Asian (SAS) AF: 0.758 AC: 3659 AN: 4824

European-Finnish (FIN) AF: 0.766 AC: 8102 AN: 10582

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54205 AN: 67992

Other (OTH) AF: 0.824 AC: 1740 AN: 2112

Alfa AF: 0.805 Hom.: 5759

Bravo AF: 0.820

Asia WGS AF: 0.779 AC: 2708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.54
PhyloP100		-0.076

Splicing

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

Other links and lift over

dbSNP: rs1954004; hg19: chr14-59558119;