Variant rs6434811 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_018897.3(DNAH7):c.1152G>A(p.Thr384Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 1,577,548 control chromosomes in the GnomAD database, including 612,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.72 ( 44685 hom., cov: 32)

Exomes 𝑓: 0.89 ( 567928 hom. )

Consequence

DNAH7
NM_018897.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0560

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 2-196001696-C-T is Benign according to our data. Variant chr2-196001696-C-T is described in ClinVar as [Benign]. Clinvar id is 402756.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.056 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.903 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.1152G>A	p.Thr384Thr	synonymous_variant	11/65	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.1152G>A	p.Thr384Thr	synonymous_variant	11/65	1	NM_018897.3	ENSP00000311273.6		Q8WXX0-1
DNAH7	ENST00000410072.5 linkuse as main transcript	c.1152G>A	p.Thr384Thr	synonymous_variant	11/13	2		ENSP00000386260.1		Q8WXX0-4

Frequencies

GnomAD3 genomes

AF:

0.721

AC:

109593

AN:

151970

Hom.:

44694

Cov.:

show subpopulations

Gnomad AFR

AF:

0.310

Gnomad AMI

AF:

0.924

Gnomad AMR

AF:

0.772

Gnomad ASJ

AF:

0.885

Gnomad EAS

AF:

0.662

Gnomad SAS

AF:

0.924

Gnomad FIN

AF:

0.898

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.909

Gnomad OTH

AF:

0.752

GnomAD3 exomes

AF:

0.834

AC:

191598

AN:

229846

Hom.:

82959

AF XY:

0.850

AC XY:

106036

AN XY:

124786

show subpopulations

Gnomad AFR exome

AF:

0.294

Gnomad AMR exome

AF:

0.778

Gnomad ASJ exome

AF:

0.887

Gnomad EAS exome

AF:

0.657

Gnomad SAS exome

AF:

0.921

Gnomad FIN exome

AF:

0.902

Gnomad NFE exome

AF:

0.910

Gnomad OTH exome

AF:

0.862

GnomAD4 exome

AF:

0.886

AC:

1263540

AN:

1425460

Hom.:

567928

Cov.:

AF XY:

0.890

AC XY:

627723

AN XY:

705622

show subpopulations

Gnomad4 AFR exome

AF:

0.282

Gnomad4 AMR exome

AF:

0.785

Gnomad4 ASJ exome

AF:

0.891

Gnomad4 EAS exome

AF:

0.692

Gnomad4 SAS exome

AF:

0.922

Gnomad4 FIN exome

AF:

0.897

Gnomad4 NFE exome

AF:

0.914

Gnomad4 OTH exome

AF:

0.849

GnomAD4 genome

AF:

0.721

AC:

109588

AN:

152088

Hom.:

44685

Cov.:

AF XY:

0.724

AC XY:

53853

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.309

Gnomad4 AMR

AF:

0.772

Gnomad4 ASJ

AF:

0.885

Gnomad4 EAS

AF:

0.662

Gnomad4 SAS

AF:

0.924

Gnomad4 FIN

AF:

0.898

Gnomad4 NFE

AF:

0.909

Gnomad4 OTH

AF:

0.747

Alfa

AF:

0.870

Hom.:

129920

Bravo

AF:

0.690

Asia WGS

AF:

0.749

AC:

2606

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 11, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

0.87

DANN

Benign

0.61

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