Variant rs6488908 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001372106.1(DNAH10):c.9030A>G(p.Lys3010Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0605 in 1,613,944 control chromosomes in the GnomAD database, including 3,372 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.077 ( 529 hom., cov: 33)

Exomes 𝑓: 0.059 ( 2843 hom. )

Consequence

DNAH10
NM_001372106.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.04

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 12-123893267-A-G is Benign according to our data. Variant chr12-123893267-A-G is described in ClinVar as [Benign]. Clinvar id is 402618.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-123893267-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=2.04 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH10	NM_001372106.1 linkuse as main transcript	c.9030A>G	p.Lys3010Lys	synonymous_variant	53/79	ENST00000673944.1	NP_001359035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
DNAH10	ENST00000673944.1 linkuse as main transcript	c.9030A>G	p.Lys3010Lys	synonymous_variant	53/79		NM_001372106.1	ENSP00000501095.1	A0A669KB38
DNAH10	ENST00000409039.8 linkuse as main transcript	c.8859A>G	p.Lys2953Lys	synonymous_variant	52/78	5		ENSP00000386770.4	A0A1C7CYW8
DNAH10	ENST00000638045.1 linkuse as main transcript	c.8676A>G	p.Lys2892Lys	synonymous_variant	52/78	5		ENSP00000489675.1	Q8IVF4-1

Frequencies

GnomAD3 genomes

AF:

0.0765

AC:

11643

AN:

152188

Hom.:

528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.106

Gnomad AMR

AF:

0.0512

Gnomad ASJ

AF:

0.0389

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0271

Gnomad FIN

AF:

0.0691

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0623

Gnomad OTH

AF:

0.0774

GnomAD3 exomes

AF:

0.0548

AC:

13645

AN:

249066

Hom.:

504

AF XY:

0.0543

AC XY:

7338

AN XY:

135136

show subpopulations

Gnomad AFR exome

AF:

0.133

Gnomad AMR exome

AF:

0.0331

Gnomad ASJ exome

AF:

0.0344

Gnomad EAS exome

AF:

0.000946

Gnomad SAS exome

AF:

0.0285

Gnomad FIN exome

AF:

0.0671

Gnomad NFE exome

AF:

0.0656

Gnomad OTH exome

AF:

0.0597

GnomAD4 exome

AF:

0.0588

AC:

86013

AN:

1461638

Hom.:

2843

Cov.:

AF XY:

0.0580

AC XY:

42170

AN XY:

727102

show subpopulations

Gnomad4 AFR exome

AF:

0.132

Gnomad4 AMR exome

AF:

0.0349

Gnomad4 ASJ exome

AF:

0.0364

Gnomad4 EAS exome

AF:

0.000730

Gnomad4 SAS exome

AF:

0.0299

Gnomad4 FIN exome

AF:

0.0712

Gnomad4 NFE exome

AF:

0.0619

Gnomad4 OTH exome

AF:

0.0586

GnomAD4 genome

AF:

0.0766

AC:

11663

AN:

152306

Hom.:

529

Cov.:

AF XY:

0.0736

AC XY:

5486

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.129

Gnomad4 AMR

AF:

0.0511

Gnomad4 ASJ

AF:

0.0389

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0269

Gnomad4 FIN

AF:

0.0691

Gnomad4 NFE

AF:

0.0623

Gnomad4 OTH

AF:

0.0766

Alfa

AF:

0.0684

Hom.:

307

Bravo

AF:

0.0781

Asia WGS

AF:

0.0270

AC:

AN:

3478

EpiCase

AF:

0.0602

EpiControl

AF:

0.0584

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

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

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

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

8.0

DANN

Benign

0.53

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