Variant rs75859635 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018897.3(DNAH7):c.6340A>G(p.Thr2114Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0368 in 1,531,804 control chromosomes in the GnomAD database, including 1,169 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.031 ( 94 hom., cov: 32)

Exomes 𝑓: 0.037 ( 1075 hom. )

Consequence

DNAH7
NM_018897.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 4.91

Variant links:

Genes affected

DNAH7 (HGNC:18661): (dynein axonemal heavy chain 7) DNAH7 is a component of the inner dynein arm of ciliary axonemes (Zhang et al., 2002 [PubMed 11877439]).[supplied by OMIM, Mar 2008]

DNAH7 links:

DNAH7 (HGNC:):

DNAH7 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 (MetaRNN=0.007309526).

BP6

Variant 2-195873641-T-C is Benign according to our data. Variant chr2-195873641-T-C is described in ClinVar as [Benign]. Clinvar id is 402749.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-195873641-T-C is described in Lovd as [Benign].

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH7	NM_018897.3 linkuse as main transcript	c.6340A>G	p.Thr2114Ala	missense_variant	39/65	ENST00000312428.11	NP_061720.2	Q8WXX0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH7	ENST00000312428.11 linkuse as main transcript	c.6340A>G	p.Thr2114Ala	missense_variant	39/65	1	NM_018897.3	ENSP00000311273.6		Q8WXX0-1

Frequencies

GnomAD3 genomes

AF:

0.0312

AC:

4751

AN:

152086

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0168

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.0300

Gnomad ASJ

AF:

0.0294

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0108

Gnomad FIN

AF:

0.0365

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0427

Gnomad OTH

AF:

0.0346

GnomAD3 exomes

AF:

0.0303

AC:

5804

AN:

191358

Hom.:

126

AF XY:

0.0317

AC XY:

3342

AN XY:

105542

show subpopulations

Gnomad AFR exome

AF:

0.0158

Gnomad AMR exome

AF:

0.0178

Gnomad ASJ exome

AF:

0.0321

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0158

Gnomad FIN exome

AF:

0.0339

Gnomad NFE exome

AF:

0.0407

Gnomad OTH exome

AF:

0.0319

GnomAD4 exome

AF:

0.0374

AC:

51645

AN:

1379600

Hom.:

1075

Cov.:

AF XY:

0.0370

AC XY:

25347

AN XY:

685046

show subpopulations

Gnomad4 AFR exome

AF:

0.0168

Gnomad4 AMR exome

AF:

0.0202

Gnomad4 ASJ exome

AF:

0.0316

Gnomad4 EAS exome

AF:

0.0000560

Gnomad4 SAS exome

AF:

0.0161

Gnomad4 FIN exome

AF:

0.0354

Gnomad4 NFE exome

AF:

0.0413

Gnomad4 OTH exome

AF:

0.0355

GnomAD4 genome

AF:

0.0312

AC:

4750

AN:

152204

Hom.:

Cov.:

AF XY:

0.0304

AC XY:

2263

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0167

Gnomad4 AMR

AF:

0.0300

Gnomad4 ASJ

AF:

0.0294

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0108

Gnomad4 FIN

AF:

0.0365

Gnomad4 NFE

AF:

0.0427

Gnomad4 OTH

AF:

0.0343

Alfa

AF:

0.0401

Hom.:

205

Bravo

AF:

0.0311

TwinsUK

AF:

0.0399

AC:

148

ALSPAC

AF:

0.0413

AC:

159

ESP6500AA

AF:

0.0144

AC:

ESP6500EA

AF:

0.0434

AC:

353

ExAC

AF:

0.0307

AC:

3712

Asia WGS

AF:

0.00780

AC:

AN:

3476

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

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.012

Eigen

Benign

-0.26

Eigen_PC

Benign

-0.022

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.85

MetaRNN

Benign

0.0073

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.81

PrimateAI

Benign

0.48

PROVEAN

Benign

-1.7

REVEL

Benign

0.13

Sift

Benign

0.41

Polyphen

0.019

Vest4

0.29

MPC

0.035

ClinPred

0.0069

GERP RS

4.8

Varity_R

0.35

gMVP

0.50

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