Genetic Variant NM_001372.4:c.12106-10C>T (chr17-11932004-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_001372.4(DNAH9):c.12106-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 1,612,952 control chromosomes in the GnomAD database, including 25,633 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2354 hom., cov: 32)

Exomes 𝑓: 0.18 ( 23279 hom. )

Consequence

DNAH9
NM_001372.4 intron

Scores

Splicing: ADA: 0.00002495

Clinical Significance

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

Conservation

PhyloP100: -0.130

Variant links:

Genes affected

DNAH9 (HGNC:2953): (dynein axonemal heavy chain 9) This gene encodes the heavy chain subunit of axonemal dynein, a large multi-subunit molecular motor. Axonemal dynein attaches to microtubules and hydrolyzes ATP to mediate the movement of cilia and flagella. The gene expresses at least two transcript variants; additional variants have been described, but their full length nature has not been determined. [provided by RefSeq, Jul 2008]

DNAH9 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 17-11932004-C-T is Benign according to our data. Variant chr17-11932004-C-T is described in ClinVar as [Benign]. Clinvar id is 402786.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH9	NM_001372.4 link	c.12106-10C>T		intron_variant	Intron 63 of 68	ENST00000262442.9	NP_001363.2	Q9NYC9-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAH9	ENST00000262442.9 link	c.12106-10C>T	intron_variant	Intron 63 of 68	1	NM_001372.4	ENSP00000262442.3	Q9NYC9-1
DNAH9	ENST00000608377.5 link	c.1042-10C>T	intron_variant	Intron 9 of 14	1		ENSP00000476951.1	Q9NYC9-3
DNAH9	ENST00000396001.6 link	n.1569-10C>T	intron_variant	Intron 9 of 14	1
DNAH9	ENST00000454412.6 link	c.11878-10C>T	intron_variant	Intron 62 of 67	5		ENSP00000414874.2	E7EP17

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26312

AN:

151956

Hom.:

2347

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.196

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.180

Gnomad OTH

AF:

0.175

GnomAD3 exomes

AF:

0.185

AC:

46446

AN:

250842

Hom.:

4587

AF XY:

0.180

AC XY:

24456

AN XY:

135552

show subpopulations

Gnomad AFR exome

AF:

0.140

Gnomad AMR exome

AF:

0.276

Gnomad ASJ exome

AF:

0.150

Gnomad EAS exome

AF:

0.194

Gnomad SAS exome

AF:

0.139

Gnomad FIN exome

AF:

0.193

Gnomad NFE exome

AF:

0.177

Gnomad OTH exome

AF:

0.184

GnomAD4 exome

AF:

0.176

AC:

257467

AN:

1460876

Hom.:

23279

Cov.:

AF XY:

0.174

AC XY:

126648

AN XY:

726644

show subpopulations

Gnomad4 AFR exome

AF:

0.142

Gnomad4 AMR exome

AF:

0.265

Gnomad4 ASJ exome

AF:

0.153

Gnomad4 EAS exome

AF:

0.181

Gnomad4 SAS exome

AF:

0.140

Gnomad4 FIN exome

AF:

0.193

Gnomad4 NFE exome

AF:

0.176

Gnomad4 OTH exome

AF:

0.175

GnomAD4 genome

AF:

0.173

AC:

26330

AN:

152076

Hom.:

2354

Cov.:

AF XY:

0.173

AC XY:

12838

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.143

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.155

Gnomad4 EAS

AF:

0.195

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.197

Gnomad4 NFE

AF:

0.180

Gnomad4 OTH

AF:

0.176

Alfa

AF:

0.180

Hom.:

3200

Bravo

AF:

0.177

Asia WGS

AF:

0.159

AC:

551

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.4

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000025

dbscSNV1_RF

Benign

0.048

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