XR_944742.4:n.1159C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490

Publications

2 publications found
Variant links:
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)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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
YEATS4XR_944742.4 linkn.1159C>A non_coding_transcript_exon_variant Exon 8 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02373ENST00000776073.1 linkn.372+173C>A intron_variant Intron 3 of 4
LINC02373ENST00000776080.1 linkn.*86C>A downstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.276
AC:
41961
AN:
151898
Hom.:
6855
Cov.:
31
show subpopulations
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
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1444
2887
4331
5774
7218
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
430
860
1290
1720
2150
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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

Publications

Other links and lift over

dbSNP: rs12367916; hg19: chr12-69818080; API