chr14-59159667-T-C

Variant names:

• chr14-59159667-T-C
• rs8016068
• ENST00000657369.1:n.716-23996T>C

Variant summary

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

The ENST00000657369.1(LINC01500):​n.716-23996T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,208 control chromosomes in the GnomAD database, including 53,052 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 0.83 (53052 hom., cov: 33)
• Consequence: LINC01500 ENST00000657369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 2 publications found

Genes affected

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

LOC107984642 (HGNC:):

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984642	XR_001750928.1	n.41+1483T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01500	ENST00000657369.1	n.716-23996T>C		intron_variant	Intron 5 of 5
LINC01500	ENST00000663641.1	n.830-23996T>C		intron_variant	Intron 5 of 5
LINC01500	ENST00000665985.1	n.693-23996T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126849 AN: 152090 Hom.: 53001 Cov.: 33

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.834 AC: 126954 AN: 152208 Hom.: 53052 Cov.: 33 AF XY: 0.830 AC XY: 61772 AN XY: 74402

African (AFR) AF: 0.860 AC: 35710 AN: 41536

American (AMR) AF: 0.804 AC: 12284 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3135 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3434 AN: 5174

South Asian (SAS) AF: 0.786 AC: 3792 AN: 4822

European-Finnish (FIN) AF: 0.845 AC: 8941 AN: 10580

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56870 AN: 68020

Other (OTH) AF: 0.846 AC: 1786 AN: 2112

Alfa AF: 0.835 Hom.: 36860

Bravo AF: 0.833

Asia WGS AF: 0.771 AC: 2682 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	2.9
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8016068; hg19: chr14-59626385;