5-13902136-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001369.3(DNAH5):c.1647C>T(p.Asn549=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000256 in 1,599,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001369.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH5 | NM_001369.3 | c.1647C>T | p.Asn549= | splice_region_variant, synonymous_variant | 13/79 | ENST00000265104.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.1647C>T | p.Asn549= | splice_region_variant, synonymous_variant | 13/79 | 1 | NM_001369.3 | P4 | |
DNAH5 | ENST00000681290.1 | c.1602C>T | p.Asn534= | splice_region_variant, synonymous_variant | 13/79 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152104Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000103 AC: 25AN: 241900Hom.: 0 AF XY: 0.0000918 AC XY: 12AN XY: 130676
GnomAD4 exome AF: 0.0000256 AC: 37AN: 1447248Hom.: 0 Cov.: 28 AF XY: 0.0000278 AC XY: 20AN XY: 720184
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74420
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 06, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at