Variant rs61587964 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.9741A>G(p.Ala3247Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 1,606,932 control chromosomes in the GnomAD database, including 53,179 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 9454 hom., cov: 32)

Exomes 𝑓: 0.24 ( 43725 hom. )

Consequence

DNAH10
NM_001372106.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.25

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=-0.8).

BP6

Variant 12-123903039-A-G is Benign according to our data. Variant chr12-123903039-A-G is described in ClinVar as [Benign]. Clinvar id is 402622.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-123903039-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-2.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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.9741A>G	p.Ala3247Ala	synonymous_variant	57/79	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.9741A>G	p.Ala3247Ala	synonymous_variant	57/79		NM_001372106.1	ENSP00000501095.1	A0A669KB38
DNAH10	ENST00000409039.8 linkuse as main transcript	c.9570A>G	p.Ala3190Ala	synonymous_variant	56/78	5		ENSP00000386770.4	A0A1C7CYW8
DNAH10	ENST00000638045.1 linkuse as main transcript	c.9387A>G	p.Ala3129Ala	synonymous_variant	56/78	5		ENSP00000489675.1	Q8IVF4-1

Frequencies

GnomAD3 genomes

AF:

0.323

AC:

49067

AN:

151826

Hom.:

9435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.548

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.223

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.241

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.317

GnomAD3 exomes

AF:

0.252

AC:

60052

AN:

238504

Hom.:

8132

AF XY:

0.246

AC XY:

31823

AN XY:

129182

show subpopulations

Gnomad AFR exome

AF:

0.553

Gnomad AMR exome

AF:

0.256

Gnomad ASJ exome

AF:

0.219

Gnomad EAS exome

AF:

0.252

Gnomad SAS exome

AF:

0.235

Gnomad FIN exome

AF:

0.232

Gnomad NFE exome

AF:

0.222

Gnomad OTH exome

AF:

0.249

GnomAD4 exome

AF:

0.240

AC:

348745

AN:

1454988

Hom.:

43725

Cov.:

AF XY:

0.239

AC XY:

172502

AN XY:

722996

show subpopulations

Gnomad4 AFR exome

AF:

0.565

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.267

Gnomad4 SAS exome

AF:

0.241

Gnomad4 FIN exome

AF:

0.242

Gnomad4 NFE exome

AF:

0.227

Gnomad4 OTH exome

AF:

0.261

GnomAD4 genome

AF:

0.323

AC:

49140

AN:

151944

Hom.:

9454

Cov.:

AF XY:

0.321

AC XY:

23825

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.549

Gnomad4 AMR

AF:

0.269

Gnomad4 ASJ

AF:

0.223

Gnomad4 EAS

AF:

0.270

Gnomad4 SAS

AF:

0.250

Gnomad4 FIN

AF:

0.241

Gnomad4 NFE

AF:

0.227

Gnomad4 OTH

AF:

0.315

Alfa

AF:

0.266

Hom.:

3190

Bravo

AF:

0.337

Asia WGS

AF:

0.311

AC:

1079

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

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

-0.80

CADD

Benign

0.086

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