chr9-85962005-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024635.4(NAA35):c.349-8C>A 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 0.0000499 in 1,443,676 control chromosomes in the GnomAD database, including 2 homozygotes. 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_024635.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA35 | NM_024635.4 | c.349-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000361671.10 | |||
NAA35 | NM_001321881.2 | c.349-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
NAA35 | NM_001321882.2 | c.349-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
NAA35 | XM_005252127.5 | c.349-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA35 | ENST00000361671.10 | c.349-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_024635.4 | P1 | |||
NAA35 | ENST00000376040.2 | c.349-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
NAA35 | ENST00000416045.4 | n.446-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 3AN: 151774Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.0000935 AC: 22AN: 235300Hom.: 0 AF XY: 0.000149 AC XY: 19AN XY: 127284
GnomAD4 exome AF: 0.0000499 AC: 72AN: 1443676Hom.: 2 Cov.: 29 AF XY: 0.0000822 AC XY: 59AN XY: 717746
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000198 AC: 3AN: 151890Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74232
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at