NM_020547.3:c.128dupT
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_020547.3(AMHR2):c.128dupT(p.Asp44ArgfsTer40) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,276 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
AMHR2
NM_020547.3 frameshift
NM_020547.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.43
Publications
0 publications found
Genes affected
AMHR2 (HGNC:465): (anti-Mullerian hormone receptor type 2) This gene encodes the receptor for the anti-Mullerian hormone (AMH) which, in addition to testosterone, results in male sex differentiation. AMH and testosterone are produced in the testes by different cells and have different effects. Testosterone promotes the development of male genitalia while the binding of AMH to the encoded receptor prevents the development of the mullerian ducts into uterus and Fallopian tubes. Mutations in this gene are associated with persistent Mullerian duct syndrome type II. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Sep 2009]
AMHR2 Gene-Disease associations (from GenCC):
- persistent Mullerian duct syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 12-53424365-C-CT is Pathogenic according to our data. Variant chr12-53424365-C-CT is described in ClinVar as Pathogenic. ClinVar VariationId is 1076254.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020547.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AMHR2 | NM_020547.3 | MANE Select | c.128dupT | p.Asp44ArgfsTer40 | frameshift | Exon 2 of 11 | NP_065434.1 | Q16671-1 | |
| AMHR2 | NM_001164690.2 | c.128dupT | p.Asp44ArgfsTer40 | frameshift | Exon 2 of 11 | NP_001158162.1 | Q16671-2 | ||
| AMHR2 | NM_001164691.2 | c.128dupT | p.Asp44ArgfsTer40 | frameshift | Exon 2 of 9 | NP_001158163.1 | Q16671-3 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AMHR2 | ENST00000257863.9 | TSL:1 MANE Select | c.128dupT | p.Asp44ArgfsTer40 | frameshift | Exon 2 of 11 | ENSP00000257863.3 | Q16671-1 | |
| AMHR2 | ENST00000379791.7 | TSL:1 | c.128dupT | p.Asp44ArgfsTer40 | frameshift | Exon 2 of 9 | ENSP00000369117.3 | Q16671-3 | |
| AMHR2 | ENST00000550311.5 | TSL:1 | c.128dupT | p.Asp44ArgfsTer40 | frameshift | Exon 2 of 11 | ENSP00000446661.1 | Q16671-2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.0000159 AC: 4AN: 251260 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
4
AN:
251260
AF XY:
Gnomad AFR exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461276Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726932 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1461276
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
726932
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33458
American (AMR)
AF:
AC:
4
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86212
European-Finnish (FIN)
AF:
AC:
0
AN:
53414
Middle Eastern (MID)
AF:
AC:
0
AN:
5312
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111982
Other (OTH)
AF:
AC:
0
AN:
60342
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
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Allele balance
Age Distribution
Exome Het
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
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ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
1
-
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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