Genetic Variant DNAH14:c.6749-15T>C (chr1-225252286-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_001367479.1(DNAH14):c.6749-15T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,401,128 control chromosomes in the GnomAD database, including 61,470 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 12787 hom., cov: 32)

Exomes 𝑓: 0.26 ( 48683 hom. )

Consequence

DNAH14
NM_001367479.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.566

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=-0.92).

BP6

Variant 1-225252286-T-C is Benign according to our data. Variant chr1-225252286-T-C is described in ClinVar as [Benign]. Clinvar id is 402652.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH14	NM_001367479.1 link	c.6749-15T>C		intron_variant	Intron 43 of 85	ENST00000682510.1	NP_001354408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH14	ENST00000682510.1 link	c.6749-15T>C		intron_variant	Intron 43 of 85		NM_001367479.1	ENSP00000508305.1		A0A804HLD3

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55572

AN:

151888

Hom.:

12750

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.382

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.258

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.369

GnomAD3 exomes

AF:

0.324

AC:

50385

AN:

155532

Hom.:

9939

AF XY:

0.316

AC XY:

26012

AN XY:

82372

show subpopulations

Gnomad AFR exome

AF:

0.627

Gnomad AMR exome

AF:

0.448

Gnomad ASJ exome

AF:

0.238

Gnomad EAS exome

AF:

0.623

Gnomad SAS exome

AF:

0.351

Gnomad FIN exome

AF:

0.196

Gnomad NFE exome

AF:

0.221

Gnomad OTH exome

AF:

0.287

GnomAD4 exome

AF:

0.260

AC:

324192

AN:

1249124

Hom.:

48683

Cov.:

AF XY:

0.260

AC XY:

162457

AN XY:

624182

show subpopulations

Gnomad4 AFR exome

AF:

0.634

Gnomad4 AMR exome

AF:

0.444

Gnomad4 ASJ exome

AF:

0.240

Gnomad4 EAS exome

AF:

0.586

Gnomad4 SAS exome

AF:

0.349

Gnomad4 FIN exome

AF:

0.200

Gnomad4 NFE exome

AF:

0.224

Gnomad4 OTH exome

AF:

0.292

GnomAD4 genome

AF:

0.366

AC:

55667

AN:

152004

Hom.:

12787

Cov.:

AF XY:

0.366

AC XY:

27222

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.618

Gnomad4 AMR

AF:

0.394

Gnomad4 ASJ

AF:

0.238

Gnomad4 EAS

AF:

0.607

Gnomad4 SAS

AF:

0.381

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.223

Gnomad4 OTH

AF:

0.369

Alfa

AF:

0.285

Hom.:

1682

Bravo

AF:

0.395

Asia WGS

AF:

0.508

AC:

1766

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

Mar 28, 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

1.2

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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