rs1463666

Variant names:

• chr12-127898827-A-G
• rs1463666
• NR_126452.2:n.312-13722T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-127898827-A-G
• chr12-127898827-A-T

Variant summary

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

The NR_126452.2(LINC00508):​n.312-13722T>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 NR_126452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00508	NR_126452.2	n.312-13722T>C		intron_variant	Intron 3 of 3
LINC02393	NR_033987.1	n.*188A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02393	ENST00000614177.2	n.*182A>G		downstream_gene_variant		2
LINC02393	ENST00000662498.1	n.*209A>G		downstream_gene_variant

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

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.0904

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.205

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463666; hg19: chr12-128383372;