12-127898827-A-G

Variant names:

• chr12-127898827-A-G
• rs1463666
• ENST00000741352.1:n.317-36971T>C

Variant summary

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

The ENST00000741352.1(LINC00508):​n.317-36971T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,924 control chromosomes in the GnomAD database, including 6,725 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 0.24 (6725 hom., cov: 32)
• Consequence: LINC00508 ENST00000741352.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 3 publications found

Genes affected

LINC00508 (HGNC:43559): (long intergenic non-protein coding RNA 508)

LINC02393 (HGNC:53320): (long intergenic non-protein coding RNA 2393)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741352.1. 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
	LINC00508	NR_126452.2		n.312-13722T>C		intron	N/A
	LINC02393	NR_033987.1		n.*188A>G		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00508	ENST00000741352.1		n.317-36971T>C		intron	N/A
	LINC00508	ENST00000741353.1		n.284-13722T>C		intron	N/A
	LINC00508	ENST00000741354.1		n.435-36971T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35753 AN: 151806 Hom.: 6722 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.236 AC: 35789 AN: 151924 Hom.: 6725 Cov.: 32 AF XY: 0.234 AC XY: 17356 AN XY: 74276

African (AFR) AF: 0.509 AC: 21038 AN: 41370

American (AMR) AF: 0.147 AC: 2252 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3470

East Asian (EAS) AF: 0.494 AC: 2532 AN: 5126

South Asian (SAS) AF: 0.0904 AC: 436 AN: 4822

European-Finnish (FIN) AF: 0.140 AC: 1478 AN: 10582

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7283 AN: 67968

Other (OTH) AF: 0.205 AC: 433 AN: 2110

Alfa AF: 0.178 Hom.: 652

Bravo AF: 0.252

Asia WGS AF: 0.298 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.14
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1463666; hg19: chr12-128383372;