Variant 1-225367810-C-T 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_001367479.1(DNAH14):c.12096C>T(p.Ala4032Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 1,545,532 control chromosomes in the GnomAD database, including 213,426 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 16717 hom., cov: 32)

Exomes 𝑓: 0.52 ( 196709 hom. )

Consequence

DNAH14
NM_001367479.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.81

Variant links:

Genes affected

DNAH14 (HGNC:2945): (dynein axonemal heavy chain 14) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. Two major classes of dyneins, axonemal and cytoplasmic, have been identified. DNAH14 is an axonemal dynein heavy chain (DHC) (Vaughan et al., 1996 [PubMed 8812413]).[supplied by OMIM, Mar 2008]

DNAH14 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=-0.57).

BP6

Variant 1-225367810-C-T is Benign according to our data. Variant chr1-225367810-C-T is described in ClinVar as [Benign]. Clinvar id is 402661.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.81 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH14	NM_001367479.1 linkuse as main transcript	c.12096C>T	p.Ala4032Ala	synonymous_variant	77/86	ENST00000682510.1	NP_001354408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH14	ENST00000682510.1 linkuse as main transcript	c.12096C>T	p.Ala4032Ala	synonymous_variant	77/86		NM_001367479.1	ENSP00000508305.1		A0A804HLD3

Frequencies

GnomAD3 genomes

AF:

0.445

AC:

67664

AN:

151892

Hom.:

16715

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.526

Gnomad AMR

AF:

0.463

Gnomad ASJ

AF:

0.639

Gnomad EAS

AF:

0.215

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.565

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.560

Gnomad OTH

AF:

0.476

GnomAD3 exomes

AF:

0.458

AC:

70169

AN:

153326

Hom.:

17509

AF XY:

0.456

AC XY:

37099

AN XY:

81354

show subpopulations

Gnomad AFR exome

AF:

0.247

Gnomad AMR exome

AF:

0.388

Gnomad ASJ exome

AF:

0.642

Gnomad EAS exome

AF:

0.217

Gnomad SAS exome

AF:

0.316

Gnomad FIN exome

AF:

0.560

Gnomad NFE exome

AF:

0.555

Gnomad OTH exome

AF:

0.530

GnomAD4 exome

AF:

0.522

AC:

727489

AN:

1393522

Hom.:

196709

Cov.:

AF XY:

0.518

AC XY:

356017

AN XY:

687536

show subpopulations

Gnomad4 AFR exome

AF:

0.237

Gnomad4 AMR exome

AF:

0.399

Gnomad4 ASJ exome

AF:

0.639

Gnomad4 EAS exome

AF:

0.211

Gnomad4 SAS exome

AF:

0.319

Gnomad4 FIN exome

AF:

0.565

Gnomad4 NFE exome

AF:

0.555

Gnomad4 OTH exome

AF:

0.511

GnomAD4 genome

AF:

0.445

AC:

67673

AN:

152010

Hom.:

16717

Cov.:

AF XY:

0.442

AC XY:

32804

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.463

Gnomad4 ASJ

AF:

0.639

Gnomad4 EAS

AF:

0.217

Gnomad4 SAS

AF:

0.293

Gnomad4 FIN

AF:

0.565

Gnomad4 NFE

AF:

0.560

Gnomad4 OTH

AF:

0.474

Alfa

AF:

0.527

Hom.:

9629

Bravo

AF:

0.430

Asia WGS

AF:

0.273

AC:

950

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 28, 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

-0.57

CADD

Benign

1.1

DANN

Benign

0.48

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