chr2-11578289-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_014668.4(GREB1):c.638-8C>A 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 0.00184 in 1,608,768 control chromosomes in the GnomAD database, including 56 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_014668.4 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 |
---|---|---|---|---|---|---|---|
GREB1 | NM_014668.4 | c.638-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000381486.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GREB1 | ENST00000381486.7 | c.638-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_014668.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00987 AC: 1501AN: 152124Hom.: 34 Cov.: 33
GnomAD3 exomes AF: 0.00253 AC: 633AN: 250418Hom.: 13 AF XY: 0.00186 AC XY: 252AN XY: 135330
GnomAD4 exome AF: 0.000999 AC: 1455AN: 1456526Hom.: 22 Cov.: 31 AF XY: 0.000871 AC XY: 630AN XY: 723476
GnomAD4 genome ? AF: 0.00991 AC: 1509AN: 152242Hom.: 34 Cov.: 33 AF XY: 0.00952 AC XY: 709AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at