GeneBe

rs61502519

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_018897.3(DNAH7):​c.4549-10_4549-3delTTTTTTTT variant causes a splice region, intron change. The variant allele was found at a frequency of 0.00000098 in 1,020,860 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 16)
Exomes 𝑓: 9.8e-7 ( 0 hom. )

Consequence

DNAH7
NM_018897.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.59

Publications

0 publications found
Variant links:
Genes affected
DNAH7 (HGNC:18661): (dynein axonemal heavy chain 7) DNAH7 is a component of the inner dynein arm of ciliary axonemes (Zhang et al., 2002 [PubMed 11877439]).[supplied by OMIM, Mar 2008]
DNAH7 Gene-Disease associations (from GenCC):
  • ciliary dyskinesia, primary, 50
    Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
  • male infertility with azoospermia or oligozoospermia due to single gene mutation
    Inheritance: AR Classification: LIMITED Submitted by: King Faisal Specialist Hospital and Research Center

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018897.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DNAH7
NM_018897.3
MANE Select
c.4549-10_4549-3delTTTTTTTT
splice_region intron
N/ANP_061720.2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DNAH7
ENST00000312428.11
TSL:1 MANE Select
c.4549-10_4549-3delTTTTTTTT
splice_region intron
N/AENSP00000311273.6
DNAH7
ENST00000475293.1
TSL:1
n.5482-10_5482-3delTTTTTTTT
splice_region intron
N/A

Frequencies

GnomAD3 genomes
Cov.:
16
GnomAD4 exome
AF:
9.80e-7
AC:
1
AN:
1020860
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
516148
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
22394
American (AMR)
AF:
0.00
AC:
0
AN:
23480
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19332
East Asian (EAS)
AF:
0.00
AC:
0
AN:
33328
South Asian (SAS)
AF:
0.00
AC:
0
AN:
57678
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
40658
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4352
European-Non Finnish (NFE)
AF:
0.00000129
AC:
1
AN:
775540
Other (OTH)
AF:
0.00
AC:
0
AN:
44098
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs61502519; hg19: chr2-196762491; API