chr3-128055512-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_013336.4(SEC61A1):c.76-4C>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 0.000123 in 1,607,148 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_013336.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC61A1 | NM_013336.4 | c.76-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000243253.8 | |||
SEC61A1 | NM_001400328.1 | c.94-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SEC61A1 | NM_001400329.1 | c.-84-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC61A1 | ENST00000243253.8 | c.76-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_013336.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251470Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135908
GnomAD4 exome AF: 0.000123 AC: 179AN: 1454796Hom.: 0 Cov.: 30 AF XY: 0.000126 AC XY: 91AN XY: 724168
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74504
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 01, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2017 | - - |
SEC61A1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 15, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at