GeneBe

3-149601710-ATTTTT-ATTTTTTT

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_015472.6(WWTR1):​c.432-28712_432-28711dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000040 ( 0 hom., cov: 0)

Consequence

WWTR1
NM_015472.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.144

Publications

0 publications found
Variant links:
Genes affected
WWTR1 (HGNC:24042): (WW domain containing transcription regulator 1) Enables transcription coactivator activity. Involved in several processes, including hippo signaling; positive regulation of cell differentiation; and regulation of signal transduction. Located in cytosol and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2
High AC in GnomAd4 at 6 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WWTR1NM_015472.6 linkc.432-28712_432-28711dupAA intron_variant Intron 2 of 6 ENST00000360632.8 NP_056287.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WWTR1ENST00000360632.8 linkc.432-28711_432-28710insAA intron_variant Intron 2 of 6 1 NM_015472.6 ENSP00000353847.3 Q9GZV5
WWTR1ENST00000465804.5 linkc.432-28711_432-28710insAA intron_variant Intron 3 of 7 2 ENSP00000419465.1 Q9GZV5
WWTR1ENST00000467467.5 linkc.432-28711_432-28710insAA intron_variant Intron 2 of 6 5 ENSP00000419234.1 Q9GZV5
WWTR1ENST00000479238.1 linkc.432-28711_432-28710insAA intron_variant Intron 1 of 1 3 ENSP00000418580.1 C9J038

Frequencies

GnomAD3 genomes
AF:
0.0000398
AC:
6
AN:
150662
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000731
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000659
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000210
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000398
AC:
6
AN:
150776
Hom.:
0
Cov.:
0
AF XY:
0.0000271
AC XY:
2
AN XY:
73674
show subpopulations
African (AFR)
AF:
0.0000729
AC:
3
AN:
41180
American (AMR)
AF:
0.0000658
AC:
1
AN:
15190
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3460
East Asian (EAS)
AF:
0.000194
AC:
1
AN:
5160
South Asian (SAS)
AF:
0.000210
AC:
1
AN:
4760
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10122
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
292
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67602
Other (OTH)
AF:
0.00
AC:
0
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.467
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<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:
0.00
Hom.:
1335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.14

Splicing

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

Publications

Other links and lift over

dbSNP: rs3976504; hg19: chr3-149319497; API