chr3-128052831-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_013336.4(SEC61A1):c.8-4A>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 0.00000137 in 1,460,948 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_013336.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEC61A1 | NM_013336.4 | c.8-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000243253.8 | |||
SEC61A1 | NM_001400328.1 | c.26-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SEC61A1 | NM_001400329.1 | c.-85+272A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEC61A1 | ENST00000243253.8 | c.8-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_013336.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250902Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135726
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460948Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726824
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 10, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at