11-102110869-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001130145.3(YAP1):​c.21G>A​(p.Pro7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000831 in 1,415,782 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0014 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00076 ( 2 hom. )

Consequence

YAP1
NM_001130145.3 synonymous

Scores

1
1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.294
Variant links:
Genes affected
YAP1 (HGNC:16262): (Yes1 associated transcriptional regulator) This gene encodes a downstream nuclear effector of the Hippo signaling pathway which is involved in development, growth, repair, and homeostasis. This gene is known to play a role in the development and progression of multiple cancers as a transcriptional regulator of this signaling pathway and may function as a potential target for cancer treatment. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 11-102110869-G-A is Benign according to our data. Variant chr11-102110869-G-A is described in ClinVar as [Benign]. Clinvar id is 711380.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.294 with no splicing effect.
BS2
High AC in GnomAd4 at 212 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
YAP1NM_001130145.3 linkuse as main transcriptc.21G>A p.Pro7= synonymous_variant 1/9 ENST00000282441.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
YAP1ENST00000282441.10 linkuse as main transcriptc.21G>A p.Pro7= synonymous_variant 1/91 NM_001130145.3 P2P46937-1

Frequencies

GnomAD3 genomes
AF:
0.00140
AC:
212
AN:
151644
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000197
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00384
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00236
Gnomad OTH
AF:
0.000961
GnomAD3 exomes
AF:
0.00107
AC:
73
AN:
68432
Hom.:
1
AF XY:
0.000854
AC XY:
34
AN XY:
39802
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00185
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00354
Gnomad NFE exome
AF:
0.00140
Gnomad OTH exome
AF:
0.00210
GnomAD4 exome
AF:
0.000763
AC:
964
AN:
1264030
Hom.:
2
Cov.:
31
AF XY:
0.000768
AC XY:
478
AN XY:
622490
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000448
Gnomad4 ASJ exome
AF:
0.00224
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00374
Gnomad4 NFE exome
AF:
0.000727
Gnomad4 OTH exome
AF:
0.000900
GnomAD4 genome
AF:
0.00140
AC:
212
AN:
151752
Hom.:
1
Cov.:
32
AF XY:
0.00152
AC XY:
113
AN XY:
74180
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000197
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00384
Gnomad4 NFE
AF:
0.00236
Gnomad4 OTH
AF:
0.000951
Alfa
AF:
0.00519
Hom.:
1
Bravo
AF:
0.000608

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 25, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
13
DANN
Uncertain
0.98
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.3

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs775598673; hg19: chr11-101981600; API