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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;