rs12579108

chr12-102483541-C-Achr12-102483541-C-Gchr12-102483541-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007063427.1(LINC02456):n.34555C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0335 in 152,238 control chromosomes in the GnomAD database, including 364 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 0.033 (364 hom., cov: 32)
• Consequence: LINC02456 XR_007063427.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526

Genes affected

LINC02456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.34555C>A		non_coding_transcript_exon_variant	11/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0334 AC: 5085 AN: 152120 Hom.: 362 Cov.: 32

Gnomad AFR AF: 0.00567

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0681

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.0669

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.0387

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

GnomAD4 genome AF: 0.0335 AC: 5093 AN: 152238 Hom.: 364 Cov.: 32 AF XY: 0.0384 AC XY: 2854 AN XY: 74412

Gnomad4 AFR AF: 0.00566

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.0669

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.0138

Gnomad4 OTH AF: 0.0392

Alfa AF: 0.0244 Hom.: 25

Bravo AF: 0.0337

Asia WGS AF: 0.191 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	11
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12579108; hg19: chr12-102877319;