chr12-69416372-G-T

Variant names:

• chr12-69416372-G-T
• rs17813347
• ENST00000776073.1:n.246-7629G>T

Variant summary

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

The ENST00000776073.1(LINC02373):​n.246-7629G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 152,288 control chromosomes in the GnomAD database, including 191 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 0.042 (191 hom., cov: 32)
• Consequence: LINC02373 ENST00000776073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 1 publications found

Genes affected

LINC02373 (HGNC:53295): (long intergenic non-protein coding RNA 2373)

YEATS4 (HGNC:24859): (YEATS domain containing 4) The protein encoded by this gene is found in the nucleoli. It has high sequence homology to human MLLT1, and yeast and human MLLT3 proteins. Both MLLT1 and MLLT3 proteins belong to a class of transcription factors, indicating that the encoded protein might also represent a transcription factor. This protein is thought to be required for RNA transcription. This gene has been shown to be amplified in tumors. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.063 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776073.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02373	ENST00000776073.1		n.246-7629G>T		intron	N/A
	LINC02373	ENST00000776080.1		n.-87G>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6346 AN: 152170 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0417 AC: 6344 AN: 152288 Hom.: 191 Cov.: 32 AF XY: 0.0398 AC XY: 2963 AN XY: 74466

African (AFR) AF: 0.0115 AC: 477 AN: 41558

American (AMR) AF: 0.0426 AC: 652 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4830

European-Finnish (FIN) AF: 0.0286 AC: 303 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0646 AC: 4394 AN: 68032

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

Alfa AF: 0.0590 Hom.: 383

Bravo AF: 0.0416

Asia WGS AF: 0.00751 AC: 26 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.61
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs17813347; hg19: chr12-69810152;