rs150857304
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001206927.2(DNAH8):c.9987C>T(p.Ser3329=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,604,264 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 13 hom. )
Consequence
DNAH8
NM_001206927.2 synonymous
NM_001206927.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.352
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 Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BP6
Variant 6-38915224-C-T is Benign according to our data. Variant chr6-38915224-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 414400.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.352 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00225 (342/152208) while in subpopulation NFE AF= 0.00325 (221/68016). AF 95% confidence interval is 0.0029. There are 0 homozygotes in gnomad4. There are 170 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH8 | NM_001206927.2 | c.9987C>T | p.Ser3329= | synonymous_variant | 68/93 | ENST00000327475.11 | NP_001193856.1 | |
DNAH8-AS1 | NR_038401.1 | n.783-7387G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH8 | ENST00000327475.11 | c.9987C>T | p.Ser3329= | synonymous_variant | 68/93 | 5 | NM_001206927.2 | ENSP00000333363 | P2 | |
DNAH8 | ENST00000359357.7 | c.9336C>T | p.Ser3112= | synonymous_variant | 66/91 | 2 | ENSP00000352312 | A2 | ||
DNAH8 | ENST00000449981.6 | c.9987C>T | p.Ser3329= | synonymous_variant | 67/82 | 5 | ENSP00000415331 |
Frequencies
GnomAD3 genomes AF: 0.00225 AC: 342AN: 152090Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00329 AC: 797AN: 242030Hom.: 1 AF XY: 0.00346 AC XY: 453AN XY: 131076
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GnomAD4 exome AF: 0.00272 AC: 3945AN: 1452056Hom.: 13 Cov.: 31 AF XY: 0.00268 AC XY: 1934AN XY: 722300
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GnomAD4 genome AF: 0.00225 AC: 342AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.00228 AC XY: 170AN XY: 74406
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | DNAH8: BP4, BP7 - |
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