dbSNP rs75558206: DNAH10:c.9815+9C>T (chr12-123903122-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_001372106.1(DNAH10):c.9815+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0418 in 1,600,364 control chromosomes in the GnomAD database, including 4,711 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 2119 hom., cov: 33)

Exomes 𝑓: 0.035 ( 2592 hom. )

Consequence

DNAH10
NM_001372106.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0920

Variant links:

Genes affected

DNAH10 (HGNC:2941): (dynein axonemal heavy chain 10) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. The axonemal dyneins, found in cilia and flagella, are components of the outer and inner dynein arms attached to the peripheral microtubule doublets. DNAH10 is an inner arm dynein heavy chain (Maiti et al., 2000 [PubMed 11175280]).[supplied by OMIM, Mar 2008]

DNAH10 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=-0.81).

BP6

Variant 12-123903122-C-T is Benign according to our data. Variant chr12-123903122-C-T is described in ClinVar as [Benign]. Clinvar id is 402623.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-123903122-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH10	NM_001372106.1 link	c.9815+9C>T		intron_variant	Intron 57 of 78	ENST00000673944.1	NP_001359035.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAH10	ENST00000673944.1 link	c.9815+9C>T	intron_variant	Intron 57 of 78		NM_001372106.1	ENSP00000501095.1	A0A669KB38
DNAH10	ENST00000409039.8 link	c.9644+9C>T	intron_variant	Intron 56 of 77	5		ENSP00000386770.4	A0A1C7CYW8
DNAH10	ENST00000638045.1 link	c.9461+9C>T	intron_variant	Intron 56 of 77	5		ENSP00000489675.1	Q8IVF4-1

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

16476

AN:

152080

Hom.:

2113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.0395

Gnomad AMR

AF:

0.0678

Gnomad ASJ

AF:

0.0769

Gnomad EAS

AF:

0.000964

Gnomad SAS

AF:

0.0174

Gnomad FIN

AF:

0.00434

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0277

Gnomad OTH

AF:

0.101

GnomAD3 exomes

AF:

0.0423

AC:

9608

AN:

227000

Hom.:

763

AF XY:

0.0379

AC XY:

4667

AN XY:

123070

show subpopulations

Gnomad AFR exome

AF:

0.314

Gnomad AMR exome

AF:

0.0409

Gnomad ASJ exome

AF:

0.0685

Gnomad EAS exome

AF:

0.000833

Gnomad SAS exome

AF:

0.0187

Gnomad FIN exome

AF:

0.00418

Gnomad NFE exome

AF:

0.0256

Gnomad OTH exome

AF:

0.0436

GnomAD4 exome

AF:

0.0348

AC:

50390

AN:

1448166

Hom.:

2592

Cov.:

AF XY:

0.0336

AC XY:

24155

AN XY:

718816

show subpopulations

Gnomad4 AFR exome

AF:

0.331

Gnomad4 AMR exome

AF:

0.0426

Gnomad4 ASJ exome

AF:

0.0710

Gnomad4 EAS exome

AF:

0.000613

Gnomad4 SAS exome

AF:

0.0198

Gnomad4 FIN exome

AF:

0.00422

Gnomad4 NFE exome

AF:

0.0275

Gnomad4 OTH exome

AF:

0.0506

GnomAD4 genome

AF:

0.108

AC:

16506

AN:

152198

Hom.:

2119

Cov.:

AF XY:

0.105

AC XY:

7776

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.0677

Gnomad4 ASJ

AF:

0.0769

Gnomad4 EAS

AF:

0.000966

Gnomad4 SAS

AF:

0.0172

Gnomad4 FIN

AF:

0.00434

Gnomad4 NFE

AF:

0.0277

Gnomad4 OTH

AF:

0.101

Alfa

AF:

0.0755

Hom.:

484

Bravo

AF:

0.124

Asia WGS

AF:

0.0340

AC:

118

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

Mar 29, 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 -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.9

DANN

Benign

0.22

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