12-98473938-G-A

Variant names:

• chr12-98473938-G-A
• rs249847
• ENST00000789930.1:n.160+19493C>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+19493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,854 control chromosomes in the GnomAD database, including 28,819 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 0.60 (28819 hom., cov: 31)
• Consequence: LINC02453 ENST00000789930.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 8 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 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+19493C>T		intron_variant	Intron 2 of 3
LINC02453	ENST00000789931.1	n.150+19493C>T		intron_variant	Intron 2 of 3
LINC02453	ENST00000789932.1	n.160+19493C>T		intron_variant	Intron 3 of 4
LINC02453	ENST00000789933.1	n.163+19493C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90538 AN: 151736 Hom.: 28768 Cov.: 31

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.597 AC: 90642 AN: 151854 Hom.: 28819 Cov.: 31 AF XY: 0.591 AC XY: 43827 AN XY: 74172

African (AFR) AF: 0.833 AC: 34545 AN: 41448

American (AMR) AF: 0.448 AC: 6828 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1929 AN: 3466

East Asian (EAS) AF: 0.431 AC: 2219 AN: 5146

South Asian (SAS) AF: 0.521 AC: 2505 AN: 4808

European-Finnish (FIN) AF: 0.480 AC: 5042 AN: 10514

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35574 AN: 67922

Other (OTH) AF: 0.574 AC: 1212 AN: 2110

Alfa AF: 0.545 Hom.: 13155

Bravo AF: 0.604

Asia WGS AF: 0.484 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs249847; hg19: chr12-98867716;