Variant rs62065706 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.468-28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,612,230 control chromosomes in the GnomAD database, including 18,812 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1279 hom., cov: 31)

Exomes 𝑓: 0.15 ( 17533 hom. )

Consequence

DNAI2
NM_023036.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.397

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:

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=-0.86).

BP6

Variant 17-74289566-C-T is Benign according to our data. Variant chr17-74289566-C-T is described in ClinVar as [Benign]. Clinvar id is 261652.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAI2	NM_023036.6 linkuse as main transcript	c.468-28C>T		intron_variant		ENST00000311014.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAI2	ENST00000311014.11 linkuse as main transcript	c.468-28C>T		intron_variant		1	NM_023036.6	P2	Q9GZS0-1

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18287

AN:

151466

Hom.:

1280

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0774

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.0816

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.00425

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.0737

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.109

GnomAD3 exomes

AF:

0.123

AC:

30851

AN:

250566

Hom.:

2299

AF XY:

0.128

AC XY:

17296

AN XY:

135454

show subpopulations

Gnomad AFR exome

AF:

0.0804

Gnomad AMR exome

AF:

0.0557

Gnomad ASJ exome

AF:

0.108

Gnomad EAS exome

AF:

0.00283

Gnomad SAS exome

AF:

0.131

Gnomad FIN exome

AF:

0.170

Gnomad NFE exome

AF:

0.160

Gnomad OTH exome

AF:

0.122

GnomAD4 exome

AF:

0.150

AC:

219072

AN:

1460654

Hom.:

17533

Cov.:

AF XY:

0.150

AC XY:

109317

AN XY:

726656

show subpopulations

Gnomad4 AFR exome

AF:

0.0774

Gnomad4 AMR exome

AF:

0.0579

Gnomad4 ASJ exome

AF:

0.112

Gnomad4 EAS exome

AF:

0.00179

Gnomad4 SAS exome

AF:

0.133

Gnomad4 FIN exome

AF:

0.171

Gnomad4 NFE exome

AF:

0.164

Gnomad4 OTH exome

AF:

0.126

GnomAD4 genome

AF:

0.121

AC:

18301

AN:

151576

Hom.:

1279

Cov.:

AF XY:

0.119

AC XY:

8813

AN XY:

73980

show subpopulations

Gnomad4 AFR

AF:

0.0775

Gnomad4 AMR

AF:

0.0815

Gnomad4 ASJ

AF:

0.118

Gnomad4 EAS

AF:

0.00426

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.170

Gnomad4 NFE

AF:

0.158

Gnomad4 OTH

AF:

0.108

Alfa

AF:

0.139

Hom.:

284

Bravo

AF:

0.112

Asia WGS

AF:

0.0560

AC:

196

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 24, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.4

DANN

Benign

0.35

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