rs139821753
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate
The NM_001369.3(DNAH5):c.9911C>T(p.Ser3304Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,614,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. S3304S) has been classified as Likely benign.
Frequency
Consequence
NM_001369.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH5 | NM_001369.3 | c.9911C>T | p.Ser3304Leu | missense_variant | 59/79 | ENST00000265104.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.9911C>T | p.Ser3304Leu | missense_variant | 59/79 | 1 | NM_001369.3 | P4 | |
DNAH5 | ENST00000681290.1 | c.9866C>T | p.Ser3289Leu | missense_variant | 59/79 | A1 | |||
DNAH5 | ENST00000504001.3 | n.609+2794C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250930Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135602
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461840Hom.: 0 Cov.: 32 AF XY: 0.0000523 AC XY: 38AN XY: 727232
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74366
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 17, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at