Genetic Variant DNAI1:c.1019+42C>T (chr9-34500881-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_012144.4(DNAI1):c.1019+42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,480,920 control chromosomes in the GnomAD database, including 34,461 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2524 hom., cov: 32)

Exomes 𝑓: 0.21 ( 31937 hom. )

Consequence

DNAI1
NM_012144.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0480

Variant links:

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]

DNAI1 links:

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=-0.78).

BP6

Variant 9-34500881-C-T is Benign according to our data. Variant chr9-34500881-C-T is described in ClinVar as [Benign]. Clinvar id is 260194.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAI1	NM_012144.4 link	c.1019+42C>T		intron_variant	Intron 11 of 19	ENST00000242317.9	NP_036276.1	Q9UI46-1A0A140VJI0
DNAI1	NM_001281428.2 link	c.1031+42C>T		intron_variant	Intron 11 of 19		NP_001268357.1	Q9UI46A0A087WWV9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAI1	ENST00000242317.9 link	c.1019+42C>T		intron_variant	Intron 11 of 19	1	NM_012144.4	ENSP00000242317.4		Q9UI46-1
DNAI1	ENST00000614641.4 link	c.1031+42C>T		intron_variant	Intron 11 of 19	5		ENSP00000480538.1		A0A087WWV9

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24709

AN:

152084

Hom.:

2523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0497

Gnomad AMI

AF:

0.166

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.365

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.167

GnomAD3 exomes

AF:

0.198

AC:

49513

AN:

250246

Hom.:

5816

AF XY:

0.207

AC XY:

28007

AN XY:

135338

show subpopulations

Gnomad AFR exome

AF:

0.0454

Gnomad AMR exome

AF:

0.0851

Gnomad ASJ exome

AF:

0.158

Gnomad EAS exome

AF:

0.374

Gnomad SAS exome

AF:

0.272

Gnomad FIN exome

AF:

0.175

Gnomad NFE exome

AF:

0.214

Gnomad OTH exome

AF:

0.190

GnomAD4 exome

AF:

0.212

AC:

282023

AN:

1328718

Hom.:

31937

Cov.:

AF XY:

0.215

AC XY:

143572

AN XY:

668244

show subpopulations

Gnomad4 AFR exome

AF:

0.0433

Gnomad4 AMR exome

AF:

0.0905

Gnomad4 ASJ exome

AF:

0.155

Gnomad4 EAS exome

AF:

0.368

Gnomad4 SAS exome

AF:

0.274

Gnomad4 FIN exome

AF:

0.174

Gnomad4 NFE exome

AF:

0.216

Gnomad4 OTH exome

AF:

0.198

GnomAD4 genome

AF:

0.162

AC:

24718

AN:

152202

Hom.:

2524

Cov.:

AF XY:

0.163

AC XY:

12097

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0497

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.366

Gnomad4 SAS

AF:

0.278

Gnomad4 FIN

AF:

0.178

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.171

Alfa

AF:

0.196

Hom.:

1680

Bravo

AF:

0.153

Asia WGS

AF:

0.297

AC:

1029

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Apr 10, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Kartagener syndrome

Benign:1

Jul 01, 2021

Genome-Nilou Lab

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

-0.78

CADD

Benign

6.2

DANN

Benign

0.60

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over