chr9-34514387-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_012144.4(DNAI1):c.1570-7C>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 0.000146 in 1,613,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_012144.4 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 |
---|---|---|---|---|---|---|---|
DNAI1 | NM_012144.4 | c.1570-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000242317.9 | |||
DNAI1 | NM_001281428.2 | c.1582-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAI1 | ENST00000242317.9 | c.1570-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_012144.4 |
Frequencies
GnomAD3 genomes AF: 0.000532 AC: 81AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000188 AC: 47AN: 250616Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135492
GnomAD4 exome AF: 0.000105 AC: 154AN: 1461382Hom.: 0 Cov.: 32 AF XY: 0.0000894 AC XY: 65AN XY: 727030
GnomAD4 genome AF: 0.000532 AC: 81AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74484
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at