Variant chr17-74312271-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_023036.6(DNAI2):c.1722+41C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 528,754 control chromosomes in the GnomAD database, including 214,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.85 ( 55673 hom., cov: 26)

Exomes 𝑓: 0.91 ( 158555 hom. )

Consequence

DNAI2
NM_023036.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.38

Variant links:

Genes affected

DNAI2 (HGNC:18744): (dynein axonemal intermediate chain 2) The protein encoded by this gene belongs to the dynein intermediate chain family, and is part of the dynein complex of respiratory cilia and sperm flagella. Mutations in this gene are associated with primary ciliary dyskinesia type 9. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2010]

DNAI2 links:

DNAI2 (HGNC:):

DNAI2 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=-0.93).

BP6

Variant 17-74312271-C-T is Benign according to our data. Variant chr17-74312271-C-T is described in ClinVar as [Benign]. Clinvar id is 261646.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAI2	NM_023036.6 linkuse as main transcript	c.1722+41C>T		intron_variant		ENST00000311014.11	NP_075462.3	Q9GZS0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAI2	ENST00000311014.11 linkuse as main transcript	c.1722+41C>T		intron_variant		1	NM_023036.6	ENSP00000308312.6		Q9GZS0-1

Frequencies

GnomAD3 genomes

AF:

0.854

AC:

127903

AN:

149728

Hom.:

55657

Cov.:

show subpopulations

Gnomad AFR

AF:

0.666

Gnomad AMI

AF:

0.942

Gnomad AMR

AF:

0.912

Gnomad ASJ

AF:

0.905

Gnomad EAS

AF:

0.889

Gnomad SAS

AF:

0.931

Gnomad FIN

AF:

0.924

Gnomad MID

AF:

0.867

Gnomad NFE

AF:

0.933

Gnomad OTH

AF:

0.852

GnomAD3 exomes

AF:

0.917

AC:

130211

AN:

141956

Hom.:

60047

AF XY:

0.920

AC XY:

70474

AN XY:

76612

show subpopulations

Gnomad AFR exome

AF:

0.654

Gnomad AMR exome

AF:

0.951

Gnomad ASJ exome

AF:

0.899

Gnomad EAS exome

AF:

0.897

Gnomad SAS exome

AF:

0.932

Gnomad FIN exome

AF:

0.929

Gnomad NFE exome

AF:

0.936

Gnomad OTH exome

AF:

0.921

GnomAD4 exome

AF:

0.908

AC:

344005

AN:

378910

Hom.:

158555

Cov.:

AF XY:

0.912

AC XY:

187738

AN XY:

205936

show subpopulations

Gnomad4 AFR exome

AF:

0.560

Gnomad4 AMR exome

AF:

0.947

Gnomad4 ASJ exome

AF:

0.894

Gnomad4 EAS exome

AF:

0.882

Gnomad4 SAS exome

AF:

0.929

Gnomad4 FIN exome

AF:

0.926

Gnomad4 NFE exome

AF:

0.921

Gnomad4 OTH exome

AF:

0.886

GnomAD4 genome

AF:

0.854

AC:

127963

AN:

149844

Hom.:

55673

Cov.:

AF XY:

0.857

AC XY:

62503

AN XY:

72952

show subpopulations

Gnomad4 AFR

AF:

0.665

Gnomad4 AMR

AF:

0.913

Gnomad4 ASJ

AF:

0.905

Gnomad4 EAS

AF:

0.889

Gnomad4 SAS

AF:

0.931

Gnomad4 FIN

AF:

0.924

Gnomad4 NFE

AF:

0.932

Gnomad4 OTH

AF:

0.853

Alfa

AF:

0.895

Hom.:

14364

Bravo

AF:

0.844

Asia WGS

AF:

0.896

AC:

3116

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

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Primary ciliary dyskinesia 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.0020

DANN

Benign

0.70

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