chr17-7719726-G-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020877.5(DNAH2):c.-9G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,461,856 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: 31)
Exomes 𝑓: 0.000033 ( 0 hom. )
Consequence
DNAH2
NM_020877.5 5_prime_UTR
NM_020877.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0110
Genes affected
DNAH2 (HGNC:2948): (dynein axonemal heavy chain 2) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. The axonemal dyneins, found in cilia and flagella, are components of the outer and inner dynein arms attached to the peripheral microtubule doublets. DNAH2 is an axonemal inner arm dynein heavy chain (Chapelin et al., 1997 [PubMed 9256245]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 17-7719726-G-T is Benign according to our data. Variant chr17-7719726-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3047735.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH2 | NM_020877.5 | c.-9G>T | 5_prime_UTR_variant | 2/86 | ENST00000572933.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH2 | ENST00000572933.6 | c.-9G>T | 5_prime_UTR_variant | 2/86 | 2 | NM_020877.5 | P1 | ||
DNAH2 | ENST00000570791.5 | c.-9G>T | 5_prime_UTR_variant | 2/14 | 1 | ||||
DNAH2 | ENST00000389173.6 | c.-9G>T | 5_prime_UTR_variant | 1/85 | 2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
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31
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250358Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135634
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GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727232
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GnomAD4 genome Cov.: 31
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
DNAH2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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