14-59163821-T-C

Variant names:

• chr14-59163821-T-C
• rs6573249
• ENST00000657369.1:n.716-19842T>C

Variant summary

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

The ENST00000657369.1(LINC01500):​n.716-19842T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,110 control chromosomes in the GnomAD database, including 40,802 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 0.73 (40802 hom., cov: 32)
• Consequence: LINC01500 ENST00000657369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657369.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01500	ENST00000657369.1		n.716-19842T>C		intron	N/A
	LINC01500	ENST00000663641.1		n.830-19842T>C		intron	N/A
	LINC01500	ENST00000665985.1		n.693-19842T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111144 AN: 151992 Hom.: 40751 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.731 AC: 111250 AN: 152110 Hom.: 40802 Cov.: 32 AF XY: 0.726 AC XY: 53943 AN XY: 74350

African (AFR) AF: 0.786 AC: 32647 AN: 41510

American (AMR) AF: 0.709 AC: 10834 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2896 AN: 3472

East Asian (EAS) AF: 0.662 AC: 3431 AN: 5184

South Asian (SAS) AF: 0.675 AC: 3253 AN: 4818

European-Finnish (FIN) AF: 0.671 AC: 7083 AN: 10554

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48714 AN: 67988

Other (OTH) AF: 0.729 AC: 1536 AN: 2108

Alfa AF: 0.722 Hom.: 40699

Bravo AF: 0.740

Asia WGS AF: 0.712 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.88
PhyloP100		0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6573249;

hg19: chr14-59630539;

COSMIC: COSV53415569;