7-741343-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017802.4(DNAAF5):​c.906-4T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 1,585,028 control chromosomes in the GnomAD database, including 525,722 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 46900 hom., cov: 35)
Exomes 𝑓: 0.82 ( 478822 hom. )

Consequence

DNAAF5
NM_017802.4 splice_region, intron

Scores

2
Splicing: ADA: 0.00002695
2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -2.09
Variant links:
Genes affected
DNAAF5 (HGNC:26013): (dynein axonemal assembly factor 5) The protein encoded by this gene is essential for the preassembly or stability of axonemal dynein arms, and is found only in organisms with motile cilia and flagella. Mutations in this gene are associated with primary ciliary dyskinesia-18, a disorder characterized by abnormalities of motile cilia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Feb 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 7-741343-T-G is Benign according to our data. Variant chr7-741343-T-G is described in ClinVar as [Benign]. Clinvar id is 260939.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-741343-T-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DNAAF5NM_017802.4 linkc.906-4T>G splice_region_variant, intron_variant Intron 3 of 12 ENST00000297440.11 NP_060272.3 Q86Y56-1B3KPE2
DNAAF5XM_024446813.2 linkc.906-4T>G splice_region_variant, intron_variant Intron 3 of 11 XP_024302581.1
DNAAF5NR_075098.2 linkn.866-4T>G splice_region_variant, intron_variant Intron 3 of 12

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DNAAF5ENST00000297440.11 linkc.906-4T>G splice_region_variant, intron_variant Intron 3 of 12 1 NM_017802.4 ENSP00000297440.6 Q86Y56-1
DNAAF5ENST00000440747.5 linkc.309-4T>G splice_region_variant, intron_variant Intron 3 of 12 2 ENSP00000403165.1 H0Y650
DNAAF5ENST00000437419.5 linkc.222-4T>G splice_region_variant, intron_variant Intron 2 of 4 5 ENSP00000410788.1 H7C3B1
DNAAF5ENST00000438961.1 linkn.375-4T>G splice_region_variant, intron_variant Intron 3 of 4 4

Frequencies

GnomAD3 genomes
AF:
0.782
AC:
118999
AN:
152116
Hom.:
46863
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.710
Gnomad AMI
AF:
0.844
Gnomad AMR
AF:
0.814
Gnomad ASJ
AF:
0.855
Gnomad EAS
AF:
0.630
Gnomad SAS
AF:
0.872
Gnomad FIN
AF:
0.767
Gnomad MID
AF:
0.848
Gnomad NFE
AF:
0.821
Gnomad OTH
AF:
0.819
GnomAD3 exomes
AF:
0.802
AC:
168499
AN:
210076
Hom.:
67982
AF XY:
0.811
AC XY:
91385
AN XY:
112660
show subpopulations
Gnomad AFR exome
AF:
0.730
Gnomad AMR exome
AF:
0.737
Gnomad ASJ exome
AF:
0.860
Gnomad EAS exome
AF:
0.654
Gnomad SAS exome
AF:
0.868
Gnomad FIN exome
AF:
0.777
Gnomad NFE exome
AF:
0.837
Gnomad OTH exome
AF:
0.832
GnomAD4 exome
AF:
0.816
AC:
1169273
AN:
1432796
Hom.:
478822
Cov.:
32
AF XY:
0.818
AC XY:
580841
AN XY:
710182
show subpopulations
Gnomad4 AFR exome
AF:
0.715
Gnomad4 AMR exome
AF:
0.745
Gnomad4 ASJ exome
AF:
0.859
Gnomad4 EAS exome
AF:
0.607
Gnomad4 SAS exome
AF:
0.865
Gnomad4 FIN exome
AF:
0.773
Gnomad4 NFE exome
AF:
0.827
Gnomad4 OTH exome
AF:
0.810
GnomAD4 genome
AF:
0.782
AC:
119092
AN:
152232
Hom.:
46900
Cov.:
35
AF XY:
0.780
AC XY:
58057
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.710
Gnomad4 AMR
AF:
0.813
Gnomad4 ASJ
AF:
0.855
Gnomad4 EAS
AF:
0.629
Gnomad4 SAS
AF:
0.872
Gnomad4 FIN
AF:
0.767
Gnomad4 NFE
AF:
0.821
Gnomad4 OTH
AF:
0.822
Alfa
AF:
0.802
Hom.:
17624
Bravo
AF:
0.781
Asia WGS
AF:
0.778
AC:
2707
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:2
-
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 29, 2016
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Primary ciliary dyskinesia Benign:2
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 07, 2016
Ambry Genetics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as 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. -

Primary ciliary dyskinesia 18 Benign:1
Jul 14, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Benign:1
Nov 12, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.14
DANN
Benign
0.30
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000027
dbscSNV1_RF
Benign
0.0020
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: rs6943337; hg19: chr7-780980; COSMIC: COSV52417763; API