rs12455580

Variant names:

• chr18-77926067-T-C
• rs12455580
• ENST00000819455.1:n.93-1330A>G

Variant summary

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

The ENST00000819455.1(LINC01029):​n.93-1330A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,106 control chromosomes in the GnomAD database, including 22,113 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 0.51 (22113 hom., cov: 32)
• Consequence: LINC01029 ENST00000819455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 2 publications found

Genes affected

LINC01029 (HGNC:49015): (long intergenic non-protein coding RNA 1029)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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
LINC01029	ENST00000819455.1	n.93-1330A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77784 AN: 151988 Hom.: 22123 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.511 AC: 77786 AN: 152106 Hom.: 22113 Cov.: 32 AF XY: 0.517 AC XY: 38427 AN XY: 74376

African (AFR) AF: 0.241 AC: 10004 AN: 41510

American (AMR) AF: 0.581 AC: 8876 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1807 AN: 3466

East Asian (EAS) AF: 0.673 AC: 3484 AN: 5176

South Asian (SAS) AF: 0.547 AC: 2635 AN: 4818

European-Finnish (FIN) AF: 0.685 AC: 7242 AN: 10574

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41843 AN: 67966

Other (OTH) AF: 0.522 AC: 1101 AN: 2110

Alfa AF: 0.590 Hom.: 74301

Bravo AF: 0.495

Asia WGS AF: 0.613 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.58
DANN	Benign	0.35
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs12455580; hg19: chr18-75638023;