XR_944742.4:n.1159C>A

Variant names:

• chr12-69424300-C-A
• rs12367916
• XR_944742.4:n.1159C>A

Variant summary

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

The XR_944742.4(YEATS4):​n.1159C>A 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 0.276 in 152,014 control chromosomes in the GnomAD database, including 6,859 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 0.28 (6859 hom., cov: 31)
• Consequence: YEATS4 XR_944742.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 2 publications found

Genes affected

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]

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

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 (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YEATS4	XR_944742.4	n.1159C>A		non_coding_transcript_exon_variant	Exon 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02373	ENST00000776073.1	n.372+173C>A		intron_variant	Intron 3 of 4
LINC02373	ENST00000776080.1	n.*86C>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41961 AN: 151898 Hom.: 6855 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.276 AC: 41961 AN: 152014 Hom.: 6859 Cov.: 31 AF XY: 0.272 AC XY: 20216 AN XY: 74302

African (AFR) AF: 0.104 AC: 4332 AN: 41474

American (AMR) AF: 0.337 AC: 5147 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1036 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1254 AN: 5160

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4814

European-Finnish (FIN) AF: 0.267 AC: 2816 AN: 10562

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24972 AN: 67950

Other (OTH) AF: 0.285 AC: 602 AN: 2112

Alfa AF: 0.330 Hom.: 16355

Bravo AF: 0.272

Asia WGS AF: 0.235 AC: 817 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	6.0
DANN	Benign	0.62
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs12367916; hg19: chr12-69818080;