chr12-64043443-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_020762.4(SRGAP1):c.673-4C>G 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 0.000862 in 1,608,424 control chromosomes in the GnomAD database, including 10 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_020762.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRGAP1 | NM_020762.4 | c.673-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000355086.8 | |||
SRGAP1 | NM_001346201.2 | c.673-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SRGAP1 | XM_024449096.2 | c.673-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SRGAP1 | XM_024449097.2 | c.673-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRGAP1 | ENST00000355086.8 | c.673-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020762.4 | A1 | |||
ENST00000535594.1 | n.134-503G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00447 AC: 680AN: 152134Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00122 AC: 300AN: 246358Hom.: 4 AF XY: 0.000910 AC XY: 121AN XY: 133000
GnomAD4 exome AF: 0.000485 AC: 706AN: 1456172Hom.: 6 Cov.: 30 AF XY: 0.000401 AC XY: 290AN XY: 724056
GnomAD4 genome AF: 0.00447 AC: 680AN: 152252Hom.: 4 Cov.: 32 AF XY: 0.00449 AC XY: 334AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at