chr12-64897514-G-A

Variant names:

• chr12-64897514-G-A
• rs1445442
• ENST00000674281.1:n.*1471+12214G>A

Variant summary

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

The ENST00000674281.1(ENSG00000288591):​n.*1471+12214G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,942 control chromosomes in the GnomAD database, including 7,958 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 0.31 (7958 hom., cov: 32)
• Consequence: ENSG00000288591 ENST00000674281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 11 publications found

Genes affected

ENSG00000288591 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02389	NR_033988.1	n.93-3063G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288591	ENST00000674281.1	n.*1471+12214G>A		intron_variant	Intron 16 of 16			ENSP00000501395.1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47572 AN: 151824 Hom.: 7954 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.313 AC: 47609 AN: 151942 Hom.: 7958 Cov.: 32 AF XY: 0.321 AC XY: 23819 AN XY: 74244

African (AFR) AF: 0.209 AC: 8673 AN: 41436

American (AMR) AF: 0.339 AC: 5172 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1077 AN: 3472

East Asian (EAS) AF: 0.603 AC: 3109 AN: 5154

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4814

European-Finnish (FIN) AF: 0.389 AC: 4104 AN: 10546

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22635 AN: 67944

Other (OTH) AF: 0.310 AC: 652 AN: 2106

Alfa AF: 0.319 Hom.: 3467

Bravo AF: 0.305

Asia WGS AF: 0.442 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.55
DANN	Benign	0.42
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs1445442; hg19: chr12-65291294;