rs2790308
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001271870.5(SRGAP2B):c.261-8167T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 23)
Consequence
SRGAP2B
NM_001271870.5 intron
NM_001271870.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.83
Genes affected
SRGAP2B (HGNC:35237): (SLIT-ROBO Rho GTPase activating protein 2B) This locus encodes a member of the SLIT-ROBO Rho GTPase activating protein family. This human-specific locus resulted from incomplete segmental duplication of the SLIT-ROBO Rho GTPase activating protein 2 locus. The encoded protein lacks the GTPase activating protein domain compared to proteins encoded by SLIT-ROBO Rho GTPase activating protein 2. The functionality of the protein encoded by this locus has been questioned, as several normal individuals with homozygous deletions for this locus have been identified, and the expression of this locus appears to be much lower than the similar SLIT-ROBO Rho GTPase activating protein 2C (SRGAP2C) locus. The SRGAP2C locus has been shown to encode a protein that functions antagonistically to SLIT-ROBO Rho GTPase activating protein 2 in cortical neuron development. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRGAP2B | NM_001271870.5 | c.261-8167T>A | intron_variant | ENST00000641863.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRGAP2B | ENST00000641863.3 | c.261-8167T>A | intron_variant | NM_001271870.5 | A2 | ||||
SRGAP2B | ENST00000612199.4 | c.261-8167T>A | intron_variant | 1 | P2 | ||||
SRGAP2B | ENST00000619678.2 | c.261-3370T>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 23
GnomAD4 genome
?
Cov.:
23
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at