chr12-69432249-A-G

Variant names:

• chr12-69432249-A-G
• rs10784780
• ENST00000776073.1:n.372+8122A>G

Variant summary

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

The ENST00000776073.1(LINC02373):​n.372+8122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,778 control chromosomes in the GnomAD database, including 23,358 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 0.55 (23358 hom., cov: 30)
• Consequence: LINC02373 ENST00000776073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 3 publications found

Genes affected

LINC02373 (HGNC:53295): (long intergenic non-protein coding RNA 2373)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776073.1. 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
	LINC02373	ENST00000776073.1		n.372+8122A>G		intron	N/A
	LINC02373	ENST00000776074.1		n.176+536A>G		intron	N/A
	LINC02373	ENST00000776075.1		n.155+536A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83124 AN: 151660 Hom.: 23332 Cov.: 30

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.548 AC: 83201 AN: 151778 Hom.: 23358 Cov.: 30 AF XY: 0.552 AC XY: 40945 AN XY: 74154

African (AFR) AF: 0.444 AC: 18385 AN: 41370

American (AMR) AF: 0.600 AC: 9144 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2004 AN: 3466

East Asian (EAS) AF: 0.826 AC: 4248 AN: 5140

South Asian (SAS) AF: 0.713 AC: 3415 AN: 4792

European-Finnish (FIN) AF: 0.535 AC: 5633 AN: 10532

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38614 AN: 67932

Other (OTH) AF: 0.560 AC: 1181 AN: 2108

Alfa AF: 0.564 Hom.: 38525

Bravo AF: 0.542

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.4
DANN	Benign	0.80
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10784780; hg19: chr12-69826029;