1-225080644-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001367479.1(DNAH14):​c.3032G>T​(p.Arg1011Leu) 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. 14/17 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. R1011Q) has been classified as Benign.

Frequency

Genomes: not found (cov: 33)

Consequence

DNAH14
NM_001367479.1 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.59
Variant links:
Genes affected
DNAH14 (HGNC:2945): (dynein axonemal heavy chain 14) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. Two major classes of dyneins, axonemal and cytoplasmic, have been identified. DNAH14 is an axonemal dynein heavy chain (DHC) (Vaughan et al., 1996 [PubMed 8812413]).[supplied by OMIM, Mar 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.052168578).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DNAH14NM_001367479.1 linkc.3032G>T p.Arg1011Leu missense_variant Exon 19 of 86 ENST00000682510.1 NP_001354408.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DNAH14ENST00000682510.1 linkc.3032G>T p.Arg1011Leu missense_variant Exon 19 of 86 NM_001367479.1 ENSP00000508305.1 A0A804HLD3
DNAH14ENST00000430092.5 linkc.3032G>T p.Arg1011Leu missense_variant Exon 19 of 84 5 ENSP00000414402.1 Q0VDD8-4
DNAH14ENST00000439375.6 linkc.3032G>T p.Arg1011Leu missense_variant Exon 18 of 83 5 ENSP00000392061.2 Q0VDD8-4
DNAH14ENST00000445597.6 linkc.2834G>T p.Arg945Leu missense_variant Exon 15 of 61 5 ENSP00000409472.2 Q0VDD8-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
55
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.095
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
0.015
DANN
Benign
0.89
DEOGEN2
Benign
0.0067
T;.;.
Eigen
Benign
-1.9
Eigen_PC
Benign
-1.9
FATHMM_MKL
Benign
0.0071
N
LIST_S2
Benign
0.27
T;T;.
M_CAP
Benign
0.054
D
MetaRNN
Benign
0.052
T;T;T
MetaSVM
Benign
-1.0
T
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-1.4
N;N;N
REVEL
Benign
0.019
Sift
Benign
0.14
T;T;T
Sift4G
Benign
0.12
T;T;T
Polyphen
0.0
.;B;B
Vest4
0.13
MutPred
0.46
.;Loss of MoRF binding (P = 0.0102);Loss of MoRF binding (P = 0.0102);
MVP
0.16
ClinPred
0.068
T
GERP RS
-6.7
Varity_R
0.039

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3128652; hg19: chr1-225268346; API