chr2-195771721-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_018897.3(DNAH7):c.11372G>A(p.Arg3791Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,461,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
DNAH7
NM_018897.3 missense
NM_018897.3 missense
Scores
6
8
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.31
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.761
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH7 | NM_018897.3 | c.11372G>A | p.Arg3791Gln | missense_variant | 61/65 | ENST00000312428.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH7 | ENST00000312428.11 | c.11372G>A | p.Arg3791Gln | missense_variant | 61/65 | 1 | NM_018897.3 | P1 | |
DNAH7 | ENST00000409063.5 | c.821G>A | p.Arg274Gln | missense_variant | 6/10 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249528Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135378
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GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461852Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727230
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GnomAD4 genome Cov.: 32
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32
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Pathogenic
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;.
Polyphen
1.0
.;D
Vest4
MutPred
0.62
.;Loss of MoRF binding (P = 0.0141);
MVP
MPC
0.25
ClinPred
D
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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