rs117061525
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001206927.2(DNAH8):āc.2549A>Gā(p.Glu850Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000818 in 1,610,202 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.00083 ( 1 hom., cov: 33)
Exomes š: 0.00082 ( 16 hom. )
Consequence
DNAH8
NM_001206927.2 missense
NM_001206927.2 missense
Scores
6
8
Clinical Significance
Conservation
PhyloP100: 6.99
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.006804198).
BP6
?
Variant 6-38786918-A-G is Benign according to our data. Variant chr6-38786918-A-G is described in ClinVar as [Benign]. Clinvar id is 238639.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000834 (127/152286) while in subpopulation EAS AF= 0.0228 (118/5184). AF 95% confidence interval is 0.0194. There are 1 homozygotes in gnomad4. There are 71 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 16 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH8 | NM_001206927.2 | c.2549A>G | p.Glu850Gly | missense_variant | 18/93 | ENST00000327475.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH8 | ENST00000327475.11 | c.2549A>G | p.Glu850Gly | missense_variant | 18/93 | 5 | NM_001206927.2 | P2 | |
DNAH8 | ENST00000359357.7 | c.1898A>G | p.Glu633Gly | missense_variant | 16/91 | 2 | A2 | ||
DNAH8 | ENST00000449981.6 | c.2549A>G | p.Glu850Gly | missense_variant | 17/82 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000841 AC: 128AN: 152168Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00187 AC: 464AN: 248460Hom.: 2 AF XY: 0.00171 AC XY: 230AN XY: 134276
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GnomAD4 exome AF: 0.000816 AC: 1190AN: 1457916Hom.: 16 Cov.: 30 AF XY: 0.000840 AC XY: 609AN XY: 724914
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GnomAD4 genome ? AF: 0.000834 AC: 127AN: 152286Hom.: 1 Cov.: 33 AF XY: 0.000953 AC XY: 71AN XY: 74470
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
REVEL
Benign
Polyphen
0.014
.;.;B
Vest4
MVP
MPC
0.20
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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