12-102564295-C-A

Variant names:

• chr12-102564295-C-A
• rs855203
• ENST00000737486.1:n.121+19929C>A

Variant summary

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

The ENST00000737486.1(ENSG00000296233):​n.121+19929C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,074 control chromosomes in the GnomAD database, including 60,297 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 0.89 (60297 hom., cov: 29)
• Consequence: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 6 publications found

Genes affected

ENSG00000296233 (HGNC:):

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+80407C>A		intron_variant	Intron 11 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296233	ENST00000737486.1	n.121+19929C>A		intron_variant	Intron 1 of 3
ENSG00000296233	ENST00000737487.1	n.121+19929C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135278 AN: 151956 Hom.: 60256 Cov.: 29

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.890 AC: 135377 AN: 152074 Hom.: 60297 Cov.: 29 AF XY: 0.893 AC XY: 66380 AN XY: 74334

African (AFR) AF: 0.860 AC: 35649 AN: 41474

American (AMR) AF: 0.925 AC: 14149 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2941 AN: 3464

East Asian (EAS) AF: 0.953 AC: 4920 AN: 5162

South Asian (SAS) AF: 0.898 AC: 4316 AN: 4806

European-Finnish (FIN) AF: 0.913 AC: 9651 AN: 10568

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60755 AN: 67996

Other (OTH) AF: 0.901 AC: 1902 AN: 2112

Alfa AF: 0.893 Hom.: 44649

Bravo AF: 0.892

Asia WGS AF: 0.946 AC: 3289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.086
DANN	Benign	0.44
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs855203; hg19: chr12-102958073;