chr14-58722643-G-A

Variant names:

• chr14-58722643-G-A
• rs17094983
• ENST00000648996.1:n.536+29237G>A

Variant summary

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

The ENST00000648996.1(LINC01500):​n.536+29237G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,072 control chromosomes in the GnomAD database, including 1,239 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 0.12 (1239 hom., cov: 32)
• Consequence: LINC01500 ENST00000648996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 24 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648996.1. 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	ENST00000648996.1		n.536+29237G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18570 AN: 151954 Hom.: 1241 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.122 AC: 18573 AN: 152072 Hom.: 1239 Cov.: 32 AF XY: 0.120 AC XY: 8954 AN XY: 74356

African (AFR) AF: 0.137 AC: 5696 AN: 41462

American (AMR) AF: 0.107 AC: 1638 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.114 AC: 549 AN: 4800

European-Finnish (FIN) AF: 0.117 AC: 1233 AN: 10576

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8473 AN: 67994

Other (OTH) AF: 0.122 AC: 257 AN: 2112

Alfa AF: 0.124 Hom.: 1138

Bravo AF: 0.122

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.3
DANN	Benign	0.66
PhyloP100		1.0

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: rs17094983;

hg19: chr14-59189361;