9-91214431-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001698.3(AUH):c.943-6T>C variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.0000301 in 1,596,728 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 Benign (★).
Frequency
Consequence
NM_001698.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AUH | NM_001698.3 | c.943-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000375731.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AUH | ENST00000375731.9 | c.943-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001698.3 | P1 | |||
AUH | ENST00000303617.5 | c.856-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
AUH | ENST00000473695.1 | n.167-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152254Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000193 AC: 44AN: 227606Hom.: 0 AF XY: 0.000170 AC XY: 21AN XY: 123392
GnomAD4 exome AF: 0.0000312 AC: 45AN: 1444474Hom.: 0 Cov.: 29 AF XY: 0.0000306 AC XY: 22AN XY: 717996
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Submissions by phenotype
3-methylglutaconic aciduria type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at