chrX-64190089-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_152424.4(AMER1):c.3198C>T(p.Gly1066=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000733 in 1,091,911 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 22)
Exomes 𝑓: 0.0000073 ( 0 hom. 5 hem. )
Consequence
AMER1
NM_152424.4 synonymous
NM_152424.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.12
Genes affected
AMER1 (HGNC:26837): (APC membrane recruitment protein 1) The protein encoded by this gene upregulates trancriptional activation by the Wilms tumor protein and interacts with many other proteins, including CTNNB1, APC, AXIN1, and AXIN2. Defects in this gene are a cause of osteopathia striata with cranial sclerosis (OSCS). [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant X-64190089-G-A is Benign according to our data. Variant chrX-64190089-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2867219.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.12 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMER1 | NM_152424.4 | c.3198C>T | p.Gly1066= | synonymous_variant | 2/2 | ENST00000374869.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMER1 | ENST00000374869.8 | c.3198C>T | p.Gly1066= | synonymous_variant | 2/2 | 5 | NM_152424.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
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22
GnomAD3 exomes AF: 0.00000609 AC: 1AN: 164094Hom.: 0 AF XY: 0.0000188 AC XY: 1AN XY: 53270
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GnomAD4 exome AF: 0.00000733 AC: 8AN: 1091911Hom.: 0 Cov.: 35 AF XY: 0.0000140 AC XY: 5AN XY: 358047
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GnomAD4 genome ? Cov.: 22
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 29, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at