rs201752275
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000420323.7(DNAH1):c.10216G>A(p.Val3406Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00271 in 1,613,144 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000420323.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH1 | NM_015512.5 | c.10216G>A | p.Val3406Ile | missense_variant | 64/78 | ENST00000420323.7 | NP_056327.4 | |
DNAH1 | XM_017006129.2 | c.10285G>A | p.Val3429Ile | missense_variant | 66/80 | XP_016861618.1 | ||
DNAH1 | XM_017006130.2 | c.10216G>A | p.Val3406Ile | missense_variant | 65/79 | XP_016861619.1 | ||
DNAH1 | XM_017006131.2 | c.10159G>A | p.Val3387Ile | missense_variant | 65/79 | XP_016861620.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH1 | ENST00000420323.7 | c.10216G>A | p.Val3406Ile | missense_variant | 64/78 | 1 | NM_015512.5 | ENSP00000401514 | P1 | |
DNAH1 | ENST00000486752.5 | n.10673G>A | non_coding_transcript_exon_variant | 63/77 | 2 | |||||
DNAH1 | ENST00000488988.5 | n.2002G>A | non_coding_transcript_exon_variant | 11/25 | 2 | |||||
DNAH1 | ENST00000490713.5 | c.916G>A | p.Val306Ile | missense_variant, NMD_transcript_variant | 7/20 | 5 | ENSP00000419071 |
Frequencies
GnomAD3 genomes AF: 0.00187 AC: 285AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00266 AC: 656AN: 246858Hom.: 2 AF XY: 0.00295 AC XY: 396AN XY: 134018
GnomAD4 exome AF: 0.00280 AC: 4090AN: 1460882Hom.: 14 Cov.: 33 AF XY: 0.00291 AC XY: 2111AN XY: 726658
GnomAD4 genome AF: 0.00187 AC: 285AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.00211 AC XY: 157AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | DNAH1: BP4 - |
Spermatogenic failure 18;C4539798:Ciliary dyskinesia, primary, 37 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 09, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at