chr12-64065207-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_020762.4(SRGAP1):c.1113C>T(p.Ile371=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000546 in 1,612,792 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0030 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00029 ( 2 hom. )
Consequence
SRGAP1
NM_020762.4 synonymous
NM_020762.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.776
Genes affected
SRGAP1 (HGNC:17382): (SLIT-ROBO Rho GTPase activating protein 1) The protein encoded by this gene is a GTPase activator, working with the GTPase CDC42 to negatively regulate neuronal migration. The encoded protein interacts with the transmembrane receptor ROBO1 to inactivate CDC42. [provided by RefSeq, Sep 2016]
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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=-0.25).
BP6
?
Variant 12-64065207-C-T is Benign according to our data. Variant chr12-64065207-C-T is described in ClinVar as [Benign]. Clinvar id is 710135.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.776 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRGAP1 | NM_020762.4 | c.1113C>T | p.Ile371= | synonymous_variant | 8/22 | ENST00000355086.8 | |
SRGAP1 | NM_001346201.2 | c.1113C>T | p.Ile371= | synonymous_variant | 8/22 | ||
SRGAP1 | XM_024449096.2 | c.1113C>T | p.Ile371= | synonymous_variant | 8/14 | ||
SRGAP1 | XM_024449097.2 | c.1113C>T | p.Ile371= | synonymous_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRGAP1 | ENST00000355086.8 | c.1113C>T | p.Ile371= | synonymous_variant | 8/22 | 1 | NM_020762.4 | A1 | |
ENST00000535594.1 | n.134-22267G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00302 AC: 459AN: 152092Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.000687 AC: 171AN: 248800Hom.: 0 AF XY: 0.000483 AC XY: 65AN XY: 134460
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GnomAD4 exome AF: 0.000287 AC: 419AN: 1460582Hom.: 2 Cov.: 30 AF XY: 0.000249 AC XY: 181AN XY: 726558
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GnomAD4 genome ? AF: 0.00304 AC: 462AN: 152210Hom.: 3 Cov.: 32 AF XY: 0.00290 AC XY: 216AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
SRGAP1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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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