rs60290948

Variant summary

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

The NM_001277115.2(DNAH11):​c.2275-15G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00505 in 1,521,768 control chromosomes in the GnomAD database, including 464 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0065 ( 63 hom., cov: 32)
Exomes 𝑓: 0.0049 ( 401 hom. )

Consequence

DNAH11
NM_001277115.2 splice_polypyrimidine_tract, intron

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -2.44
Variant links:
Genes affected
DNAH11 (HGNC:2942): (dynein axonemal heavy chain 11) This gene encodes a ciliary outer dynein arm protein and is a member of the dynein heavy chain family. It is a microtubule-dependent motor ATPase and has been reported to be involved in the movement of respiratory cilia. Mutations in this gene have been implicated in causing Kartagener Syndrome (a combination of situs inversus totalis and Primary Ciliary Dyskinesia (PCD), also called Immotile Cilia Syndrome 1 (ICS1)) and male sterility. [provided by RefSeq, Mar 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 7-21591170-G-T is Benign according to our data. Variant chr7-21591170-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 226584.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21591170-G-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DNAH11NM_001277115.2 linkuse as main transcriptc.2275-15G>T splice_polypyrimidine_tract_variant, intron_variant ENST00000409508.8 NP_001264044.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DNAH11ENST00000409508.8 linkuse as main transcriptc.2275-15G>T splice_polypyrimidine_tract_variant, intron_variant 5 NM_001277115.2 ENSP00000475939 P1

Frequencies

GnomAD3 genomes
AF:
0.00653
AC:
994
AN:
152116
Hom.:
65
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00118
Gnomad ASJ
AF:
0.00230
Gnomad EAS
AF:
0.159
Gnomad SAS
AF:
0.0133
Gnomad FIN
AF:
0.00302
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000368
Gnomad OTH
AF:
0.00624
GnomAD3 exomes
AF:
0.0144
AC:
2675
AN:
186316
Hom.:
185
AF XY:
0.0131
AC XY:
1323
AN XY:
100658
show subpopulations
Gnomad AFR exome
AF:
0.0000695
Gnomad AMR exome
AF:
0.000150
Gnomad ASJ exome
AF:
0.00329
Gnomad EAS exome
AF:
0.158
Gnomad SAS exome
AF:
0.00972
Gnomad FIN exome
AF:
0.00403
Gnomad NFE exome
AF:
0.000645
Gnomad OTH exome
AF:
0.00622
GnomAD4 exome
AF:
0.00489
AC:
6695
AN:
1369534
Hom.:
401
Cov.:
30
AF XY:
0.00481
AC XY:
3245
AN XY:
673986
show subpopulations
Gnomad4 AFR exome
AF:
0.0000663
Gnomad4 AMR exome
AF:
0.000210
Gnomad4 ASJ exome
AF:
0.00241
Gnomad4 EAS exome
AF:
0.133
Gnomad4 SAS exome
AF:
0.00785
Gnomad4 FIN exome
AF:
0.00358
Gnomad4 NFE exome
AF:
0.000258
Gnomad4 OTH exome
AF:
0.00938
GnomAD4 genome
AF:
0.00653
AC:
994
AN:
152234
Hom.:
63
Cov.:
32
AF XY:
0.00755
AC XY:
562
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.000241
Gnomad4 AMR
AF:
0.00118
Gnomad4 ASJ
AF:
0.00230
Gnomad4 EAS
AF:
0.159
Gnomad4 SAS
AF:
0.0131
Gnomad4 FIN
AF:
0.00302
Gnomad4 NFE
AF:
0.000368
Gnomad4 OTH
AF:
0.00617
Alfa
AF:
0.00135
Hom.:
0
Bravo
AF:
0.00729

ClinVar

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

Submissions by phenotype

not specified Benign:2
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineFeb 21, 20132275-15G>T in intron 13 of DNAH11: This variant is not expected to have clinical significance because it has been identified in 21.5% (43/200) of Han Chinese ch romosomes from a broad population by the 1000 Genomes Project (http://www.ncbi.n lm.nih.gov/projects/SNP; dbSNP rs60290948). -
Primary ciliary dyskinesia Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxNov 12, 2018- -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.012
DANN
Benign
0.24

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: rs60290948; hg19: chr7-21630788; COSMIC: COSV60990900; API