rs12579108

Variant names:

• chr12-102483541-C-A
• rs12579108
• XR_007063427.1:n.34555C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-102483541-C-A
• chr12-102483541-C-G
• chr12-102483541-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34555C>A		non_coding_transcript_exon_variant	Exon 11 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.00566 AC: 235 AN: 41554

American (AMR) AF: 0.0686 AC: 1048 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1556 AN: 5162

South Asian (SAS) AF: 0.0669 AC: 323 AN: 4826

European-Finnish (FIN) AF: 0.0848 AC: 898 AN: 10586

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0138 AC: 940 AN: 68030

Other (OTH) AF: 0.0392 AC: 83 AN: 2116

Alfa AF: 0.0220 Hom.: 40

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
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs12579108; hg19: chr12-102877319;