chr12-98471193-G-A

Variant names:

• chr12-98471193-G-A
• rs249851
• ENST00000789930.1:n.160+22238C>T

Variant summary

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

The ENST00000789930.1(LINC02453):​n.160+22238C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,896 control chromosomes in the GnomAD database, including 3,555 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 0.21 (3555 hom., cov: 31)
• Consequence: LINC02453 ENST00000789930.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 5 publications found

Genes affected

LINC02453 (HGNC:53392): (long intergenic non-protein coding RNA 2453)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02453	ENST00000789930.1	n.160+22238C>T		intron_variant	Intron 2 of 3
LINC02453	ENST00000789931.1	n.150+22238C>T		intron_variant	Intron 2 of 3
LINC02453	ENST00000789932.1	n.160+22238C>T		intron_variant	Intron 3 of 4
LINC02453	ENST00000789933.1	n.163+22238C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31727 AN: 151778 Hom.: 3554 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0783

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.209 AC: 31742 AN: 151896 Hom.: 3555 Cov.: 31 AF XY: 0.205 AC XY: 15213 AN XY: 74232

African (AFR) AF: 0.277 AC: 11481 AN: 41394

American (AMR) AF: 0.175 AC: 2677 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3468

East Asian (EAS) AF: 0.0787 AC: 407 AN: 5170

South Asian (SAS) AF: 0.214 AC: 1028 AN: 4798

European-Finnish (FIN) AF: 0.132 AC: 1393 AN: 10550

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13125 AN: 67946

Other (OTH) AF: 0.207 AC: 437 AN: 2108

Alfa AF: 0.201 Hom.: 1745

Bravo AF: 0.215

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs249851; hg19: chr12-98864971;