chr7-770470-G-A
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1PM2PP3_Strong
The NM_017802.4(DNAAF5):c.1784-1G>A variant causes a splice acceptor change. The variant allele was found at a frequency of 0.000000685 in 1,460,516 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_017802.4 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAAF5 | NM_017802.4 | c.1784-1G>A | splice_acceptor_variant | ENST00000297440.11 | |||
DNAAF5 | XM_024446813.2 | c.1784-1G>A | splice_acceptor_variant | ||||
DNAAF5 | NR_075098.2 | n.1744-1G>A | splice_acceptor_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAAF5 | ENST00000297440.11 | c.1784-1G>A | splice_acceptor_variant | 1 | NM_017802.4 | P1 | |||
DNAAF5 | ENST00000403952.3 | c.59-1G>A | splice_acceptor_variant | 1 | |||||
DNAAF5 | ENST00000440747.5 | c.1188-1G>A | splice_acceptor_variant | 2 | |||||
DNAAF5 | ENST00000491496.1 | n.69-1G>A | splice_acceptor_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 247982Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134370
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460516Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726548
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at