chr14-58722643-G-A

Position:

• chr14-58722643-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648996.1(LINC01500):​n.536+29237G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01500	ENST00000648996.1	n.536+29237G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.122

Alfa AF: 0.128 Hom.: 412

Bravo AF: 0.122

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17094983; hg19: chr14-59189361;