chr1-37561685-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003462.5(DNALI1):āc.526A>Gā(p.Met176Val) variant causes a missense change. The variant allele was found at a frequency of 0.000201 in 1,614,042 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 Uncertain significance (ā ).
Frequency
Genomes: š 0.00022 ( 0 hom., cov: 32)
Exomes š: 0.00020 ( 0 hom. )
Consequence
DNALI1
NM_003462.5 missense
NM_003462.5 missense
Scores
4
13
Clinical Significance
Conservation
PhyloP100: 4.37
Genes affected
DNALI1 (HGNC:14353): (dynein axonemal light intermediate chain 1) This gene is the human homolog of the Chlamydomonas inner dynein arm gene, p28. The precise function of this gene is not known, however, it is a potential candidate for immotile cilia syndrome (ICS). Ultrastructural defects of the inner dynein arms are seen in patients with ICS. Immotile mutant strains of Chlamydomonas, a biflagellated algae, exhibit similar defects. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2265484).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNALI1 | NM_003462.5 | c.526A>G | p.Met176Val | missense_variant | 4/6 | ENST00000652629.1 | NP_003453.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNALI1 | ENST00000652629.1 | c.526A>G | p.Met176Val | missense_variant | 4/6 | NM_003462.5 | ENSP00000498620 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152170Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000151 AC: 38AN: 251056Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135726
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GnomAD4 exome AF: 0.000199 AC: 291AN: 1461872Hom.: 0 Cov.: 31 AF XY: 0.000208 AC XY: 151AN XY: 727232
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GnomAD4 genome AF: 0.000217 AC: 33AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74338
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | The c.592A>G (p.M198V) alteration is located in exon 4 (coding exon 4) of the DNALI1 gene. This alteration results from a A to G substitution at nucleotide position 592, causing the methionine (M) at amino acid position 198 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
MPC
ClinPred
T
GERP RS
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