12-108506243-A-T

Variant names:

• chr12-108506243-A-T
• rs1072577
• ENST00000670674.1:n.159-5576T>A

Variant summary

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

The ENST00000670674.1(LINC01498):​n.159-5576T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,108 control chromosomes in the GnomAD database, including 24,522 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 0.56 (24522 hom., cov: 33)
• Consequence: LINC01498 ENST00000670674.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 publications found

Genes affected

LINC01498 (HGNC:51164): (long intergenic non-protein coding RNA 1498)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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
LINC01498	ENST00000670674.1	n.159-5576T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85475 AN: 151990 Hom.: 24499 Cov.: 33

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.562 AC: 85539 AN: 152108 Hom.: 24522 Cov.: 33 AF XY: 0.570 AC XY: 42367 AN XY: 74332

African (AFR) AF: 0.484 AC: 20067 AN: 41480

American (AMR) AF: 0.679 AC: 10378 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1927 AN: 3472

East Asian (EAS) AF: 0.762 AC: 3952 AN: 5186

South Asian (SAS) AF: 0.606 AC: 2920 AN: 4818

European-Finnish (FIN) AF: 0.635 AC: 6710 AN: 10568

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37797 AN: 67982

Other (OTH) AF: 0.570 AC: 1203 AN: 2110

Alfa AF: 0.541 Hom.: 2814

Bravo AF: 0.567

Asia WGS AF: 0.667 AC: 2318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.60
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1072577; hg19: chr12-108900020;