chr14-39042878-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_006364.4(SEC23A):c.1900-6C>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 0.000034 in 1,587,078 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_006364.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC23A | NM_006364.4 | c.1900-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000307712.11 | |||
SEC23A | XM_005267262.2 | c.1972-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SEC23A | XM_011536355.4 | c.1972-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SEC23A | XM_017020928.3 | c.1900-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC23A | ENST00000307712.11 | c.1900-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006364.4 | P1 | |||
SEC23A | ENST00000537403.5 | c.1294-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
SEC23A | ENST00000545328.6 | c.1813-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000178 AC: 27AN: 151738Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251320Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135852
GnomAD4 exome AF: 0.0000188 AC: 27AN: 1435218Hom.: 0 Cov.: 27 AF XY: 0.0000182 AC XY: 13AN XY: 715756
GnomAD4 genome ? AF: 0.000178 AC: 27AN: 151860Hom.: 0 Cov.: 33 AF XY: 0.000216 AC XY: 16AN XY: 74230
ClinVar
Submissions by phenotype
Craniolenticulosutural dysplasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at