chr5-13752284-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_001369.3(DNAH5):c.10878G>A(p.Thr3626Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,613,980 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001369.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.10878G>A | p.Thr3626Thr | synonymous_variant | Exon 64 of 79 | 1 | NM_001369.3 | ENSP00000265104.4 | ||
DNAH5 | ENST00000681290.1 | c.10833G>A | p.Thr3611Thr | synonymous_variant | Exon 64 of 79 | ENSP00000505288.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152148Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000136 AC: 34AN: 250806Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135524
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461714Hom.: 1 Cov.: 32 AF XY: 0.0000770 AC XY: 56AN XY: 727170
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152266Hom.: 1 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74450
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
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This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not specified Benign:1
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Primary ciliary dyskinesia 3 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at