Variant chr1-225257950-G-T 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_001367479.1(DNAH14):c.6866-10G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,529,598 control chromosomes in the GnomAD database, including 64,297 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 12768 hom., cov: 32)

Exomes 𝑓: 0.26 ( 51529 hom. )

Consequence

DNAH14
NM_001367479.1 intron

Scores

Splicing: ADA: 0.00001947

Clinical Significance

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

Conservation

PhyloP100: 0.188

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 1-225257950-G-T is Benign according to our data. Variant chr1-225257950-G-T is described in ClinVar as [Benign]. Clinvar id is 402653.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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.6866-10G>T		intron_variant		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.6866-10G>T		intron_variant			NM_001367479.1	ENSP00000508305.1		A0A804HLD3

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55491

AN:

151026

Hom.:

12732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.618

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.372

GnomAD3 exomes

AF:

0.317

AC:

45596

AN:

143998

Hom.:

8817

AF XY:

0.309

AC XY:

23540

AN XY:

76266

show subpopulations

Gnomad AFR exome

AF:

0.619

Gnomad AMR exome

AF:

0.439

Gnomad ASJ exome

AF:

0.232

Gnomad EAS exome

AF:

0.616

Gnomad SAS exome

AF:

0.346

Gnomad FIN exome

AF:

0.195

Gnomad NFE exome

AF:

0.218

Gnomad OTH exome

AF:

0.285

GnomAD4 exome

AF:

0.256

AC:

352540

AN:

1378466

Hom.:

51529

Cov.:

AF XY:

0.257

AC XY:

174502

AN XY:

679930

show subpopulations

Gnomad4 AFR exome

AF:

0.636

Gnomad4 AMR exome

AF:

0.438

Gnomad4 ASJ exome

AF:

0.239

Gnomad4 EAS exome

AF:

0.585

Gnomad4 SAS exome

AF:

0.348

Gnomad4 FIN exome

AF:

0.201

Gnomad4 NFE exome

AF:

0.223

Gnomad4 OTH exome

AF:

0.290

GnomAD4 genome

AF:

0.368

AC:

55584

AN:

151132

Hom.:

12768

Cov.:

AF XY:

0.368

AC XY:

27170

AN XY:

73736

show subpopulations

Gnomad4 AFR

AF:

0.618

Gnomad4 AMR

AF:

0.394

Gnomad4 ASJ

AF:

0.239

Gnomad4 EAS

AF:

0.607

Gnomad4 SAS

AF:

0.383

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.224

Gnomad4 OTH

AF:

0.372

Alfa

AF:

0.227

Hom.:

2163

Bravo

AF:

0.395

Asia WGS

AF:

0.508

AC:

1764

AN:

3474

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

-0.97

CADD

Benign

2.9

DANN

Benign

0.18

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000019

dbscSNV1_RF

Benign

0.0

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