12-64990190-C-T

Variant names:

• chr12-64990190-C-T
• rs6581596
• ENST00000649369.1:n.1452C>T

Variant summary

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

The ENST00000649369.1(LINC02389):​n.1452C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,034 control chromosomes in the GnomAD database, including 35,035 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 0.67 (35035 hom., cov: 31)
• Consequence: LINC02389 ENST00000649369.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 3 publications found

Genes affected

LINC02389 (HGNC:53316): (long intergenic non-protein coding RNA 2389)

LOC107984522 (HGNC:):

LINC02231 (HGNC:53100): (long intergenic non-protein coding RNA 2231)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984522	XR_001749177.2	n.1115C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02231	NR_146276.1	n.15+2087G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02389	ENST00000649369.1	n.1452C>T		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02389	ENST00000653132.1	n.1424C>T		non_coding_transcript_exon_variant	Exon 5 of 5
LINC02389	ENST00000653464.1	n.1965C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101661 AN: 151914 Hom.: 34992 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.669 AC: 101767 AN: 152034 Hom.: 35035 Cov.: 31 AF XY: 0.666 AC XY: 49492 AN XY: 74294

African (AFR) AF: 0.838 AC: 34751 AN: 41472

American (AMR) AF: 0.610 AC: 9317 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2404 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2172 AN: 5158

South Asian (SAS) AF: 0.497 AC: 2392 AN: 4810

European-Finnish (FIN) AF: 0.641 AC: 6772 AN: 10558

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41805 AN: 67980

Other (OTH) AF: 0.684 AC: 1447 AN: 2114

Alfa AF: 0.650 Hom.: 18243

Bravo AF: 0.677

Asia WGS AF: 0.535 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6581596; hg19: chr12-65383970;