12-126393285-C-G

Variant names:

• chr12-126393285-C-G
• rs918044
• XR_001749384.1:n.543C>G

Variant summary

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

The XR_001749384.1(LOC107984448):​n.543C>G 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 0.577 in 151,896 control chromosomes in the GnomAD database, including 25,896 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 0.58 (25896 hom., cov: 31)
• Consequence: LOC107984448 XR_001749384.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 3 publications found

Genes affected

LOC107984448 (HGNC:):

LINC02350 (HGNC:53272): (long intergenic non-protein coding RNA 2350)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642569.1. You can select a different transcript below to see updated ACMG assignments.

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
	LINC02350	ENST00000642569.1		n.1016-10599C>G		intron	N/A
	LINC02350	ENST00000662644.1		n.193-10599C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87459 AN: 151776 Hom.: 25843 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.577 AC: 87574 AN: 151896 Hom.: 25896 Cov.: 31 AF XY: 0.581 AC XY: 43145 AN XY: 74212

African (AFR) AF: 0.659 AC: 27306 AN: 41434

American (AMR) AF: 0.639 AC: 9755 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1632 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4460 AN: 5130

South Asian (SAS) AF: 0.604 AC: 2905 AN: 4810

European-Finnish (FIN) AF: 0.538 AC: 5673 AN: 10546

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34112 AN: 67932

Other (OTH) AF: 0.551 AC: 1162 AN: 2110

Alfa AF: 0.542 Hom.: 2808

Bravo AF: 0.590

Asia WGS AF: 0.777 AC: 2697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.36
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs918044; hg19: chr12-126877831;