dbSNP rs1316952: DNAH10:c.10722+4T>C (chr12-123915003-T-C) – 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.10722+4T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,601,102 control chromosomes in the GnomAD database, including 22,462 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 5513 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16949 hom. )

Consequence

DNAH10
NM_001372106.1 splice_region, intron

Scores

Splicing: ADA: 0.00001263

Clinical Significance

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

Conservation

PhyloP100: -4.43

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=-0.92).

BP6

Variant 12-123915003-T-C is Benign according to our data. Variant chr12-123915003-T-C is described in ClinVar as [Benign]. Clinvar id is 402624.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-123915003-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH10	NM_001372106.1 link	c.10722+4T>C		splice_region_variant, intron_variant	Intron 62 of 78	ENST00000673944.1	NP_001359035.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAH10	ENST00000673944.1 link	c.10722+4T>C	splice_region_variant, intron_variant	Intron 62 of 78		NM_001372106.1	ENSP00000501095.1	A0A669KB38
DNAH10	ENST00000409039.8 link	c.10551+4T>C	splice_region_variant, intron_variant	Intron 61 of 77	5		ENSP00000386770.4	A0A1C7CYW8
DNAH10	ENST00000638045.1 link	c.10368+4T>C	splice_region_variant, intron_variant	Intron 61 of 77	5		ENSP00000489675.1	Q8IVF4-1

Frequencies

GnomAD3 genomes

AF:

0.222

AC:

33710

AN:

152000

Hom.:

5500

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0771

Gnomad FIN

AF:

0.0884

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.220

GnomAD3 exomes

AF:

0.133

AC:

30134

AN:

225836

Hom.:

3065

AF XY:

0.129

AC XY:

15752

AN XY:

122406

show subpopulations

Gnomad AFR exome

AF:

0.472

Gnomad AMR exome

AF:

0.0986

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.00109

Gnomad SAS exome

AF:

0.0799

Gnomad FIN exome

AF:

0.0917

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.142

GnomAD4 exome

AF:

0.139

AC:

201002

AN:

1448984

Hom.:

16949

Cov.:

AF XY:

0.137

AC XY:

98291

AN XY:

719716

show subpopulations

Gnomad4 AFR exome

AF:

0.471

Gnomad4 AMR exome

AF:

0.106

Gnomad4 ASJ exome

AF:

0.242

Gnomad4 EAS exome

AF:

0.000894

Gnomad4 SAS exome

AF:

0.0810

Gnomad4 FIN exome

AF:

0.0956

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.154

GnomAD4 genome

AF:

0.222

AC:

33767

AN:

152118

Hom.:

5513

Cov.:

AF XY:

0.213

AC XY:

15878

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.460

Gnomad4 AMR

AF:

0.150

Gnomad4 ASJ

AF:

0.246

Gnomad4 EAS

AF:

0.00232

Gnomad4 SAS

AF:

0.0771

Gnomad4 FIN

AF:

0.0884

Gnomad4 NFE

AF:

0.140

Gnomad4 OTH

AF:

0.219

Alfa

AF:

0.161

Hom.:

4414

Bravo

AF:

0.241

Asia WGS

AF:

0.0770

AC:

269

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

-0.92

CADD

Benign

0.0020

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000013

dbscSNV1_RF

Benign

0.0060

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