6-39026654-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001206927.2(DNAH8):c.13823C>T(p.Thr4608Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000273 in 1,613,320 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T4608T) has been classified as Likely benign.
Frequency
Consequence
NM_001206927.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAH8 | NM_001206927.2 | c.13823C>T | p.Thr4608Met | missense_variant | 92/93 | ENST00000327475.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH8 | ENST00000327475.11 | c.13823C>T | p.Thr4608Met | missense_variant | 92/93 | 5 | NM_001206927.2 | P2 | |
DNAH8 | ENST00000359357.7 | c.13172C>T | p.Thr4391Met | missense_variant | 90/91 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00156 AC: 238AN: 152128Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000431 AC: 108AN: 250390Hom.: 0 AF XY: 0.000310 AC XY: 42AN XY: 135274
GnomAD4 exome AF: 0.000136 AC: 198AN: 1461074Hom.: 0 Cov.: 31 AF XY: 0.000113 AC XY: 82AN XY: 726762
GnomAD4 genome AF: 0.00160 AC: 243AN: 152246Hom.: 1 Cov.: 33 AF XY: 0.00165 AC XY: 123AN XY: 74436
ClinVar
Submissions by phenotype
Spermatogenic failure 46 Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 05, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 23, 2021 | - - |
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at