chr16-30064419-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001365304.2(LOC112694756):c.*407-5C>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 0.00000753 in 398,594 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_001365304.2 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 |
---|---|---|---|---|---|---|---|
LOC112694756 | NM_001365304.2 | c.*407-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000338110.11 | |||
ALDOA | NM_184043.2 | c.-108C>T | 5_prime_UTR_variant | 1/9 | |||
LOC112694756 | NM_001365305.2 | c.*407-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
LOC112694756 | NM_001365307.2 | c.*407-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000338110.11 | c.*407-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001365304.2 | P2 | ||||
ENST00000617969.1 | n.407G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000812 AC: 2AN: 246400Hom.: 0 Cov.: 0 AF XY: 0.00000801 AC XY: 1AN XY: 124854
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 26, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at