rs855203

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-102564295-C-A
• chr12-102564295-C-G

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737486.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000296233	ENST00000737486.1		n.121+19929C>A		intron	N/A
	ENSG00000296233	ENST00000737487.1		n.121+19929C>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs855203;

hg19: chr12-102958073;