rs10496313

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0610
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DNAH6NM_001370.2 linkc.662+5465A>G intron_variant Intron 4 of 76 ENST00000389394.8 NP_001361.1 Q9C0G6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DNAH6ENST00000389394.8 linkc.662+5465A>G intron_variant Intron 4 of 76 5 NM_001370.2 ENSP00000374045.3 Q9C0G6-1
DNAH6ENST00000494025.1 linkn.230-13657A>G intron_variant Intron 1 of 8 1
DNAH6ENST00000468661.1 linkn.454+8893A>G intron_variant Intron 3 of 3 4
DNAH6ENST00000476689.5 linkn.536+8893A>G intron_variant Intron 3 of 10 2

Frequencies

GnomAD3 genomes
AF:
0.0236
AC:
3580
AN:
151900
Hom.:
57
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0395
Gnomad AMI
AF:
0.0132
Gnomad AMR
AF:
0.0280
Gnomad ASJ
AF:
0.0473
Gnomad EAS
AF:
0.0114
Gnomad SAS
AF:
0.0586
Gnomad FIN
AF:
0.00388
Gnomad MID
AF:
0.0860
Gnomad NFE
AF:
0.0127
Gnomad OTH
AF:
0.0330
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0236
AC:
3588
AN:
152018
Hom.:
57
Cov.:
32
AF XY:
0.0238
AC XY:
1770
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.0395
AC:
0.0394959
AN:
0.0394959
Gnomad4 AMR
AF:
0.0280
AC:
0.0279785
AN:
0.0279785
Gnomad4 ASJ
AF:
0.0473
AC:
0.0472895
AN:
0.0472895
Gnomad4 EAS
AF:
0.0114
AC:
0.0113988
AN:
0.0113988
Gnomad4 SAS
AF:
0.0586
AC:
0.0586035
AN:
0.0586035
Gnomad4 FIN
AF:
0.00388
AC:
0.0038789
AN:
0.0038789
Gnomad4 NFE
AF:
0.0127
AC:
0.0127439
AN:
0.0127439
Gnomad4 OTH
AF:
0.0341
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:
0.0193
Hom.:
13
Bravo
AF:
0.0249
Asia WGS
AF:
0.0400
AC:
139
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.7
DANN
Benign
0.76
Mutation Taster
=100/0
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10496313; hg19: chr2-84761755; API