16-20935410-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001347886.2(DNAH3):c.11797G>A(p.Val3933Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,612,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001347886.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH3 | NM_001347886.2 | c.11797G>A | p.Val3933Ile | missense_variant | 61/62 | ENST00000698260.1 | NP_001334815.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH3 | ENST00000698260.1 | c.11797G>A | p.Val3933Ile | missense_variant | 61/62 | NM_001347886.2 | ENSP00000513632.1 | |||
DNAH3 | ENST00000261383.3 | c.11935G>A | p.Val3979Ile | missense_variant | 61/62 | 1 | ENSP00000261383.3 | |||
DNAH3 | ENST00000685858.1 | c.11977G>A | p.Val3993Ile | missense_variant | 61/62 | ENSP00000508756.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151898Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 250148Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135208
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1460550Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 726586
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151898Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74158
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.11935G>A (p.V3979I) alteration is located in exon 61 (coding exon 61) of the DNAH3 gene. This alteration results from a G to A substitution at nucleotide position 11935, causing the valine (V) at amino acid position 3979 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at