chr12-64063167-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020762.4(SRGAP1):c.1023+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000376 in 1,552,532 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
SRGAP1
NM_020762.4 intron
NM_020762.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00300
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 12-64063167-G-A is Benign according to our data. Variant chr12-64063167-G-A is described in ClinVar as [Benign]. Clinvar id is 2643158.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRGAP1 | NM_020762.4 | c.1023+29G>A | intron_variant | ENST00000355086.8 | |||
SRGAP1 | NM_001346201.2 | c.1023+29G>A | intron_variant | ||||
SRGAP1 | XM_024449096.2 | c.1023+29G>A | intron_variant | ||||
SRGAP1 | XM_024449097.2 | c.1023+29G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRGAP1 | ENST00000355086.8 | c.1023+29G>A | intron_variant | 1 | NM_020762.4 | A1 | |||
ENST00000535594.1 | n.134-20227C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00186 AC: 283AN: 152146Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000490 AC: 120AN: 245112Hom.: 0 AF XY: 0.000317 AC XY: 42AN XY: 132372
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GnomAD4 exome AF: 0.000214 AC: 300AN: 1400268Hom.: 0 Cov.: 22 AF XY: 0.000187 AC XY: 130AN XY: 695240
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GnomAD4 genome ? AF: 0.00187 AC: 284AN: 152264Hom.: 1 Cov.: 33 AF XY: 0.00187 AC XY: 139AN XY: 74452
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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 | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | SRGAP1: BS1, BS2 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at