rs795544

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000265104.5(DNAH5):​c.7888-4392T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,066 control chromosomes in the GnomAD database, including 48,907 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 0.80 ( 48907 hom., cov: 31)

Consequence

DNAH5
ENST00000265104.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09
Variant links:
Genes affected
DNAH5 (HGNC:2950): (dynein axonemal heavy chain 5) This gene encodes a dynein protein, which is part of a microtubule-associated motor protein complex consisting of heavy, light, and intermediate chains. This protein is an axonemal heavy chain dynein. It functions as a force-generating protein with ATPase activity, whereby the release of ADP is thought to produce the force-producing power stroke. Mutations in this gene cause primary ciliary dyskinesia type 3, as well as Kartagener syndrome, which are both diseases due to ciliary defects. [provided by RefSeq, Oct 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DNAH5NM_001369.3 linkuse as main transcriptc.7888-4392T>G intron_variant ENST00000265104.5 NP_001360.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DNAH5ENST00000265104.5 linkuse as main transcriptc.7888-4392T>G intron_variant 1 NM_001369.3 ENSP00000265104 P4
DNAH5ENST00000681290.1 linkuse as main transcriptc.7843-4392T>G intron_variant ENSP00000505288 A1

Frequencies

GnomAD3 genomes
AF:
0.801
AC:
121651
AN:
151948
Hom.:
48873
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.821
Gnomad AMI
AF:
0.910
Gnomad AMR
AF:
0.825
Gnomad ASJ
AF:
0.876
Gnomad EAS
AF:
0.879
Gnomad SAS
AF:
0.649
Gnomad FIN
AF:
0.697
Gnomad MID
AF:
0.877
Gnomad NFE
AF:
0.797
Gnomad OTH
AF:
0.826
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.801
AC:
121745
AN:
152066
Hom.:
48907
Cov.:
31
AF XY:
0.795
AC XY:
59113
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.821
Gnomad4 AMR
AF:
0.825
Gnomad4 ASJ
AF:
0.876
Gnomad4 EAS
AF:
0.879
Gnomad4 SAS
AF:
0.647
Gnomad4 FIN
AF:
0.697
Gnomad4 NFE
AF:
0.797
Gnomad4 OTH
AF:
0.823
Alfa
AF:
0.805
Hom.:
64538
Bravo
AF:
0.818
Asia WGS
AF:
0.742
AC:
2580
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.89
DANN
Benign
0.87

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: rs795544; hg19: chr5-13798559; API