rs1060504238
Positions:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001206927.2(DNAH8):c.2719C>T(p.Leu907=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,457,144 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 Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
DNAH8
NM_001206927.2 synonymous
NM_001206927.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.12
Genes affected
DNAH8 (HGNC:2952): (dynein axonemal heavy chain 8) The protein encoded by this gene is a heavy chain of an axonemal dynein involved in sperm and respiratory cilia motility. Axonemal dyneins generate force through hydrolysis of ATP and binding to microtubules. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 6-38790343-C-T is Benign according to our data. Variant chr6-38790343-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 414393.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.12 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH8 | NM_001206927.2 | c.2719C>T | p.Leu907= | synonymous_variant | 20/93 | ENST00000327475.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH8 | ENST00000327475.11 | c.2719C>T | p.Leu907= | synonymous_variant | 20/93 | 5 | NM_001206927.2 | P2 | |
DNAH8 | ENST00000359357.7 | c.2068C>T | p.Leu690= | synonymous_variant | 18/91 | 2 | A2 | ||
DNAH8 | ENST00000449981.6 | c.2719C>T | p.Leu907= | synonymous_variant | 19/82 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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32
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247230Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133610
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GnomAD4 exome AF: 0.0000124 AC: 18AN: 1457144Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 724900
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 18, 2016 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at