chr9-36102091-A-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_021111.3(RECK):c.1299-3A>C 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 0.00102 in 1,605,044 control chromosomes in the GnomAD database, including 20 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_021111.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RECK | NM_021111.3 | c.1299-3A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000377966.4 | |||
RECK | NM_001316345.2 | c.915-3A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
RECK | XM_017015207.2 | c.1188-3A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RECK | ENST00000377966.4 | c.1299-3A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_021111.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00530 AC: 806AN: 152016Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00140 AC: 341AN: 242806Hom.: 2 AF XY: 0.00104 AC XY: 137AN XY: 131254
GnomAD4 exome AF: 0.000576 AC: 837AN: 1452912Hom.: 13 Cov.: 31 AF XY: 0.000502 AC XY: 363AN XY: 722776
GnomAD4 genome AF: 0.00530 AC: 807AN: 152132Hom.: 7 Cov.: 32 AF XY: 0.00505 AC XY: 376AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at