ENST00000776073.1:n.246-1955T>C

Variant names:

• chr12-69422046-T-C
• rs732214
• ENST00000776073.1:n.246-1955T>C

Variant summary

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

The ENST00000776073.1(LINC02373):​n.246-1955T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,750 control chromosomes in the GnomAD database, including 11,063 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 0.37 (11063 hom., cov: 31)
• Consequence: LINC02373 ENST00000776073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YEATS4	XR_944742.4	n.860-1955T>C		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02373	ENST00000776073.1	n.246-1955T>C		intron_variant	Intron 2 of 4
LINC02373	ENST00000776080.1	n.170-1955T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56690 AN: 151632 Hom.: 11054 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.374 AC: 56740 AN: 151750 Hom.: 11063 Cov.: 31 AF XY: 0.379 AC XY: 28079 AN XY: 74150

African (AFR) AF: 0.462 AC: 19084 AN: 41338

American (AMR) AF: 0.334 AC: 5096 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3472

East Asian (EAS) AF: 0.573 AC: 2938 AN: 5126

South Asian (SAS) AF: 0.473 AC: 2275 AN: 4806

European-Finnish (FIN) AF: 0.359 AC: 3776 AN: 10532

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.311 AC: 21101 AN: 67924

Other (OTH) AF: 0.357 AC: 752 AN: 2104

Alfa AF: 0.328 Hom.: 14142

Bravo AF: 0.372

Asia WGS AF: 0.536 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs732214; hg19: chr12-69815826;