12-64016946-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020762.4(SRGAP1):c.427-4A>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000029 in 1,480,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_020762.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRGAP1 | NM_020762.4 | c.427-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000355086.8 | |||
LOC105369801 | XR_945023.3 | n.87+2747T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRGAP1 | ENST00000355086.8 | c.427-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020762.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000782 AC: 18AN: 230280Hom.: 0 AF XY: 0.0000723 AC XY: 9AN XY: 124450
GnomAD4 exome AF: 0.0000264 AC: 35AN: 1328048Hom.: 0 Cov.: 20 AF XY: 0.0000271 AC XY: 18AN XY: 665168
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74382
ClinVar
Submissions by phenotype
SRGAP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 08, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at