chr5-94888886-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_024717.7(MCTP1):c.1926C>T(p.Asp642=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00357 in 1,608,120 control chromosomes in the GnomAD database, including 89 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 29 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 60 hom. )
Consequence
MCTP1
NM_024717.7 synonymous
NM_024717.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0510
Genes affected
MCTP1 (HGNC:26183): (multiple C2 and transmembrane domain containing 1) Enables calcium ion binding activity. Predicted to be involved in several processes, including modulation of chemical synaptic transmission; negative regulation of endocytosis; and negative regulation of response to oxidative stress. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 5-94888886-G-A is Benign according to our data. Variant chr5-94888886-G-A is described in ClinVar as [Benign]. Clinvar id is 768020.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.051 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0118 (1796/152172) while in subpopulation EAS AF= 0.0446 (231/5174). AF 95% confidence interval is 0.0399. There are 29 homozygotes in gnomad4. There are 883 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 29 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCTP1 | NM_024717.7 | c.1926C>T | p.Asp642= | synonymous_variant | 12/23 | ENST00000515393.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCTP1 | ENST00000515393.6 | c.1926C>T | p.Asp642= | synonymous_variant | 12/23 | 1 | NM_024717.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0118 AC: 1796AN: 152054Hom.: 29 Cov.: 32
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GnomAD3 exomes AF: 0.00788 AC: 1978AN: 251052Hom.: 25 AF XY: 0.00632 AC XY: 857AN XY: 135672
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GnomAD4 exome AF: 0.00271 AC: 3948AN: 1455948Hom.: 60 Cov.: 29 AF XY: 0.00240 AC XY: 1736AN XY: 724818
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GnomAD4 genome ? AF: 0.0118 AC: 1796AN: 152172Hom.: 29 Cov.: 32 AF XY: 0.0119 AC XY: 883AN XY: 74418
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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 submitter | clinical testing | Invitae | May 09, 2018 | - - |
Computational scores
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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