rs10496313
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001370.2(DNAH6):c.662+5465A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 152,018 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.024 ( 57 hom., cov: 32)
Consequence
DNAH6
NM_001370.2 intron
NM_001370.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0610
Genes affected
DNAH6 (HGNC:2951): (dynein axonemal heavy chain 6) This gene belongs to the dynein family, whose members encode large proteins that are constituents of the microtubule-associated motor protein complex. This complex is composed of dynein heavy, intermediate and light chains, which can be axonemal or cytoplasmic. This protein is an axonemal dynein heavy chain. It is involved in producing force for ciliary beating by using energy from ATP hydrolysis. Mutations in this gene may cause primary ciliary dyskinesia (PCD) as well as heterotaxy. [provided by RefSeq, Jun 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.053 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH6 | ENST00000389394.8 | c.662+5465A>G | intron_variant | Intron 4 of 76 | 5 | NM_001370.2 | ENSP00000374045.3 | |||
DNAH6 | ENST00000494025.1 | n.230-13657A>G | intron_variant | Intron 1 of 8 | 1 | |||||
DNAH6 | ENST00000468661.1 | n.454+8893A>G | intron_variant | Intron 3 of 3 | 4 | |||||
DNAH6 | ENST00000476689.5 | n.536+8893A>G | intron_variant | Intron 3 of 10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0236 AC: 3580AN: 151900Hom.: 57 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3580
AN:
151900
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0236 AC: 3588AN: 152018Hom.: 57 Cov.: 32 AF XY: 0.0238 AC XY: 1770AN XY: 74312 show subpopulations
GnomAD4 genome
AF:
AC:
3588
AN:
152018
Hom.:
Cov.:
32
AF XY:
AC XY:
1770
AN XY:
74312
Gnomad4 AFR
AF:
AC:
0.0394959
AN:
0.0394959
Gnomad4 AMR
AF:
AC:
0.0279785
AN:
0.0279785
Gnomad4 ASJ
AF:
AC:
0.0472895
AN:
0.0472895
Gnomad4 EAS
AF:
AC:
0.0113988
AN:
0.0113988
Gnomad4 SAS
AF:
AC:
0.0586035
AN:
0.0586035
Gnomad4 FIN
AF:
AC:
0.0038789
AN:
0.0038789
Gnomad4 NFE
AF:
AC:
0.0127439
AN:
0.0127439
Gnomad4 OTH
AF:
AC:
0.0341232
AN:
0.0341232
Heterozygous variant carriers
0
178
357
535
714
892
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
48
96
144
192
240
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
139
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at