chr12-42717888-T-C

Variant names:

• chr12-42717888-T-C
• rs10506214
• ENST00000761458.1:n.490+9902T>C

Variant summary

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

The ENST00000761458.1(LINC02450):​n.490+9902T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,064 control chromosomes in the GnomAD database, including 4,728 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 0.24 (4728 hom., cov: 32)
• Consequence: LINC02450 ENST00000761458.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 2 publications found

Genes affected

LINC02450 (HGNC:53382): (long intergenic non-protein coding RNA 2450)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761458.1. 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
	LINC02450	ENST00000761458.1		n.490+9902T>C		intron	N/A
	LINC02450	ENST00000761459.1		n.255-18087T>C		intron	N/A
	LINC02450	ENST00000761462.1		n.41+9902T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36461 AN: 151946 Hom.: 4725 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.00445

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.240 AC: 36483 AN: 152064 Hom.: 4728 Cov.: 32 AF XY: 0.233 AC XY: 17309 AN XY: 74318

African (AFR) AF: 0.201 AC: 8338 AN: 41504

American (AMR) AF: 0.174 AC: 2658 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3466

East Asian (EAS) AF: 0.00446 AC: 23 AN: 5160

South Asian (SAS) AF: 0.229 AC: 1104 AN: 4826

European-Finnish (FIN) AF: 0.240 AC: 2534 AN: 10572

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20284 AN: 67940

Other (OTH) AF: 0.242 AC: 511 AN: 2110

Alfa AF: 0.267 Hom.: 7247

Bravo AF: 0.231

Asia WGS AF: 0.110 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.79
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10506214; hg19: chr12-43111690;