rs7971621
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020762.4(SRGAP1):c.67+21951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.971 in 151,588 control chromosomes in the GnomAD database, including 71,528 homozygotes. 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: 𝑓 0.97 ( 71528 hom., cov: 27)
Consequence
SRGAP1
NM_020762.4 intron
NM_020762.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.699
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRGAP1 | NM_020762.4 | c.67+21951G>A | intron_variant | ENST00000355086.8 | |||
SRGAP1 | NM_001346201.2 | c.67+21951G>A | intron_variant | ||||
SRGAP1 | XM_024449096.2 | c.67+21951G>A | intron_variant | ||||
SRGAP1 | XM_024449097.2 | c.67+21951G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRGAP1 | ENST00000355086.8 | c.67+21951G>A | intron_variant | 1 | NM_020762.4 | A1 | |||
SRGAP1 | ENST00000631006.3 | c.67+21951G>A | intron_variant | 5 | P3 | ||||
SRGAP1 | ENST00000695902.1 | c.67+21951G>A | intron_variant, NMD_transcript_variant | ||||||
SRGAP1 | ENST00000537556.1 | n.81+21951G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.971 AC: 147110AN: 151476Hom.: 71473 Cov.: 27
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.971 AC: 147221AN: 151588Hom.: 71528 Cov.: 27 AF XY: 0.973 AC XY: 72071AN XY: 74044
GnomAD4 genome
?
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147221
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27
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74044
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3429
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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