chr5-75379477-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001379029.1(CERT1):c.1748-4G>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 0.000101 in 1,606,810 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_001379029.1 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CERT1 | NM_001379029.1 | c.1748-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000643780.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERT1 | ENST00000643780.2 | c.1748-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001379029.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000102 AC: 25AN: 244414Hom.: 0 AF XY: 0.000113 AC XY: 15AN XY: 132430
GnomAD4 exome AF: 0.0000880 AC: 128AN: 1454574Hom.: 0 Cov.: 30 AF XY: 0.0000829 AC XY: 60AN XY: 723596
GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at