chr9-34459052-A-G

Variant names:

• chr9-34459052-A-G
• rs148701985
• NM_012144.4:c.47A>G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP3 BP6 BS1 BS2

The NM_012144.4(DNAI1):​c.47A>G​(p.Gln16Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000235 in 1,614,108 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/25 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00013 (2 hom.)
• Consequence: DNAI1 NM_012144.4 missense, splice_region
• Scores: Splicing: ADA: 0.9836
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:3
• Conservation: PhyloP100: 0.443

Genes affected

DNAI1 (HGNC:2954): (dynein axonemal intermediate chain 1) This gene encodes a member of the dynein intermediate chain family. The encoded protein is part of the dynein complex in respiratory cilia. The inner- and outer-arm dyneins, which bridge between the doublet microtubules in axonemes, are the force-generating proteins responsible for the sliding movement in axonemes. The intermediate and light chains, thought to form the base of the dynein arm, help mediate attachment and may also participate in regulating dynein activity. Mutations in this gene result in abnormal ciliary ultrastructure and function associated with primary ciliary dyskinesia and Kartagener syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, max_spliceai. No scorers claiming Uncertain. Scorers claiming Benign: dbscSNV1_RF.
• BP6: Variant 9-34459052-A-G is Benign according to our data. Variant chr9-34459052-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 228610.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=1}.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00126 (192/152316) while in subpopulation AFR AF= 0.00435 (181/41568). AF 95% confidence interval is 0.00384. There are 0 homozygotes in gnomad4. There are 100 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAI1	NM_012144.4	c.47A>G	p.Gln16Arg	missense_variant, splice_region_variant	Exon 1 of 20	ENST00000242317.9	NP_036276.1
DNAI1	NM_001281428.2	c.47A>G	p.Gln16Arg	missense_variant, splice_region_variant	Exon 1 of 20		NP_001268357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAI1	ENST00000242317.9	c.47A>G	p.Gln16Arg	missense_variant, splice_region_variant	Exon 1 of 20	1	NM_012144.4	ENSP00000242317.4
DNAI1	ENST00000614641.4	c.47A>G	p.Gln16Arg	missense_variant, splice_region_variant	Exon 1 of 20	5		ENSP00000480538.1
DNAI1	ENST00000437363.5	c.47A>G	p.Gln16Arg	missense_variant, splice_region_variant	Exon 1 of 9	5		ENSP00000395396.1
DNAI1	ENST00000470982.5	n.47+1592A>G		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.00126 AC: 192 AN: 152198 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00437

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000523

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000342 AC: 86 AN: 251352 Hom.: 0 AF XY: 0.000250 AC XY: 34 AN XY: 135862

Gnomad AFR exome AF: 0.00461

Gnomad AMR exome AF: 0.000173

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000264

Gnomad OTH exome AF: 0.000326

GnomAD4 exome AF: 0.000129 AC: 188 AN: 1461792 Hom.: 2 Cov.: 30 AF XY: 0.000111 AC XY: 81 AN XY: 727208

Gnomad4 AFR exome AF: 0.00481

Gnomad4 AMR exome AF: 0.000157

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000360

Gnomad4 OTH exome AF: 0.000232

GnomAD4 genome AF: 0.00126 AC: 192 AN: 152316 Hom.: 0 Cov.: 32 AF XY: 0.00134 AC XY: 100 AN XY: 74478

Gnomad4 AFR AF: 0.00435

Gnomad4 AMR AF: 0.000523

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.000299 Hom.: 0

Bravo AF: 0.00165

ESP6500AA AF: 0.00567 AC: 25

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000428 AC: 52

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Primary ciliary dyskinesia Benign:2

Jun 06, 2024

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely 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. -

Dec 10, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Uncertain:1

Dec 23, 2015

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant classified as Uncertain Significance - Favor Benign. The p.Gln16Arg vari ant in DNAI1 has not been previously reported in individuals with pulmonary dise ase, but has been identified in 0.45% (47/10368) of African chromosomes by the E xome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs14870 1985). Computational prediction tools and conservation analysis suggest that the p.Gln16Arg variant may not impact the protein, though this information is not p redictive enough to rule out pathogenicity. In summary, while the clinical signi ficance of the p.Gln16Arg variant is uncertain, its frequency suggests that it i s more likely to be benign. -

DNAI1-related disorder Benign:1

Mar 27, 2023

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.093
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.33
CADD	Benign	15
DANN	Benign	0.93
DEOGEN2	Benign	0.0087	T;T;T
Eigen	Benign	-0.47
Eigen_PC	Benign	-0.40
FATHMM_MKL	Benign	0.17	N
LIST_S2	Benign	0.41	T;T;T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.0062	T;T;T
MetaSVM	Benign	-0.86	T
MutationAssessor	Benign	0.34	.;.;N
PrimateAI	Benign	0.39	T
PROVEAN	Benign	0.15	.;N;N
REVEL	Benign	0.065
Sift	Benign	0.97	.;T;T
Sift4G	Benign	0.79	T;T;T
Polyphen		0.055	.;.;B
Vest4		0.18
MVP		0.77
MPC		0.13
ClinPred		0.062	T
GERP RS		1.1
Varity_R		0.053
gMVP		0.088

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.98
dbscSNV1_RF	Benign	0.72
SpliceAI score (max)		0.54		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.54		Position offset: 1

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

Publications

LitVar

Other links and lift over

dbSNP: rs148701985; hg19: chr9-34459050;