chr12-64899734-T-G

Variant names:

• chr12-64899734-T-G
• rs1144418
• ENST00000674281.1:n.*1471+14434T>G

Variant summary

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

The ENST00000674281.1(ENSG00000288591):​n.*1471+14434T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,072 control chromosomes in the GnomAD database, including 46,505 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 0.78 (46505 hom., cov: 31)
• Consequence: ENSG00000288591 ENST00000674281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02389	NR_033988.1	n.93-843T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288591	ENST00000674281.1	n.*1471+14434T>G		intron_variant	Intron 16 of 16			ENSP00000501395.1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117942 AN: 151954 Hom.: 46449 Cov.: 31

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.776 AC: 118052 AN: 152072 Hom.: 46505 Cov.: 31 AF XY: 0.776 AC XY: 57676 AN XY: 74306

African (AFR) AF: 0.919 AC: 38127 AN: 41496

American (AMR) AF: 0.740 AC: 11300 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2487 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4434 AN: 5172

South Asian (SAS) AF: 0.680 AC: 3269 AN: 4808

European-Finnish (FIN) AF: 0.711 AC: 7516 AN: 10566

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48496 AN: 67972

Other (OTH) AF: 0.768 AC: 1620 AN: 2110

Alfa AF: 0.736 Hom.: 174905

Bravo AF: 0.788

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1144418; hg19: chr12-65293514;