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GeneBe

12-123783166-G-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong

The NM_001372106.1(DNAH10):c.901G>T(p.Ala301Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A301T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

DNAH10
NM_001372106.1 missense

Scores

14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158
Variant links:
Genes affected
DNAH10 (HGNC:2941): (dynein axonemal heavy chain 10) 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. DNAH10 is an inner arm dynein heavy chain (Maiti et al., 2000 [PubMed 11175280]).[supplied by OMIM, Mar 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
PP2
?
    PP2 - Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease
Missense variant where missense usually causes diseases, DNAH10
BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (MetaRNN=0.047266036).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DNAH10NM_001372106.1 linkuse as main transcriptc.901G>T p.Ala301Ser missense_variant 7/79 ENST00000673944.1
LOC105370044XR_945481.4 linkuse as main transcriptn.495+5327C>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DNAH10ENST00000673944.1 linkuse as main transcriptc.901G>T p.Ala301Ser missense_variant 7/79 NM_001372106.1 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.082
BayesDel_addAF
Benign
-0.34
T
BayesDel_noAF
Benign
-0.72
Cadd
Benign
7.6
Dann
Benign
0.66
Eigen
Benign
-0.96
Eigen_PC
Benign
-0.85
FATHMM_MKL
Benign
0.061
N
LIST_S2
Benign
0.65
T;T;T
M_CAP
Benign
0.0031
T
MetaRNN
Benign
0.047
T;T;T
MetaSVM
Benign
-0.96
T
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.28
T
REVEL
Benign
0.026
Polyphen
0.0020
.;.;B
Vest4
0.10
MutPred
0.29
.;.;Gain of disorder (P = 0.0353);
MVP
0.15
MPC
0.13
ClinPred
0.026
T
GERP RS
3.2
Varity_R
0.030
gMVP
0.060

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-124267713; API