rs855228

Variant names:

• chr12-102503986-C-T
• rs855228
• XR_007063427.1:n.34902+20098C>T

Variant summary

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

The XR_007063427.1(LINC02456):​n.34902+20098C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,040 control chromosomes in the GnomAD database, including 39,698 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 0.70 (39698 hom., cov: 31)
• Consequence: LINC02456 XR_007063427.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106284 AN: 151922 Hom.: 39701 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.699 AC: 106307 AN: 152040 Hom.: 39698 Cov.: 31 AF XY: 0.700 AC XY: 52070 AN XY: 74342

African (AFR) AF: 0.411 AC: 17024 AN: 41410

American (AMR) AF: 0.767 AC: 11727 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2665 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3352 AN: 5148

South Asian (SAS) AF: 0.759 AC: 3658 AN: 4818

European-Finnish (FIN) AF: 0.794 AC: 8399 AN: 10584

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56995 AN: 67998

Other (OTH) AF: 0.725 AC: 1533 AN: 2114

Alfa AF: 0.759 Hom.: 9066

Bravo AF: 0.681

Asia WGS AF: 0.685 AC: 2380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs855228; hg19: chr12-102897764;