rs10506984

Variant names:

• chr12-90299488-G-C
• rs10506984
• ENST00000549470.5:n.380-711G>C

Variant summary

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

The ENST00000549470.5(LINC02392):​n.380-711G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,996 control chromosomes in the GnomAD database, including 8,634 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 0.33 (8634 hom., cov: 32)
• Consequence: LINC02392 ENST00000549470.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 3 publications found

Genes affected

LINC02392 (HGNC:53319): (long intergenic non-protein coding RNA 2392)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549470.5. 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
	LINC02392	NR_135018.1		n.380-711G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02392	ENST00000549470.5	TSL:4	n.380-711G>C		intron	N/A
	LINC02392	ENST00000658788.1		n.433-708G>C		intron	N/A
	LINC02392	ENST00000670390.1		n.430-711G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50845 AN: 151878 Hom.: 8622 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.335 AC: 50904 AN: 151996 Hom.: 8634 Cov.: 32 AF XY: 0.340 AC XY: 25259 AN XY: 74286

African (AFR) AF: 0.329 AC: 13617 AN: 41452

American (AMR) AF: 0.396 AC: 6054 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1008 AN: 3466

East Asian (EAS) AF: 0.304 AC: 1573 AN: 5168

South Asian (SAS) AF: 0.426 AC: 2049 AN: 4812

European-Finnish (FIN) AF: 0.354 AC: 3744 AN: 10574

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.320 AC: 21747 AN: 67936

Other (OTH) AF: 0.323 AC: 682 AN: 2112

Alfa AF: 0.335 Hom.: 1073

Bravo AF: 0.335

Asia WGS AF: 0.426 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.40

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: rs10506984;

hg19: chr12-90693265;