rs1554687745

Positions:

• chr9-34490108-A-G
• chr9-34490108-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_012144.4(DNAI1):​c.485A>G​(p.Asp162Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DNAI1 NM_012144.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAI1	NM_012144.4	c.485A>G	p.Asp162Gly	missense_variant	6/20	ENST00000242317.9	NP_036276.1
DNAI1	NM_001281428.2	c.497A>G	p.Asp166Gly	missense_variant	6/20		NP_001268357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAI1	ENST00000242317.9	c.485A>G	p.Asp162Gly	missense_variant	6/20	1	NM_012144.4	ENSP00000242317
DNAI1	ENST00000614641.4	c.497A>G	p.Asp166Gly	missense_variant	6/20	5		ENSP00000480538	P1
DNAI1	ENST00000437363.5	c.452A>G	p.Asp151Gly	missense_variant	5/9	5		ENSP00000395396
DNAI1	ENST00000488369.1	n.601A>G		non_coding_transcript_exon_variant	6/9	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.036	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	20
DANN	Benign	0.47
DEOGEN2	Benign	0.027	T;T;T
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.62
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.76	T;T;T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.084	T;T;T
MetaSVM	Benign	-0.94	T
MutationAssessor	Uncertain	2.1	.;.;M
MutationTaster	Benign	0.61	D
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-1.5	.;N;N
REVEL	Benign	0.26
Sift	Benign	0.39	.;T;T
Sift4G	Benign	0.14	T;T;T
Polyphen		0.0	.;.;B
Vest4		0.24
MutPred		0.17		.;.;Gain of glycosylation at S159 (P = 0.0678);
MVP		0.72
MPC		0.15
ClinPred		0.14	T
GERP RS		3.5
Varity_R		0.088
gMVP		0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.22		Position offset: 16

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554687745; hg19: chr9-34490106;