Variant 2-195897767-TAAAA-TAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018897.3(DNAH7):c.4549-3delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 6370 hom., cov: 16)

Exomes 𝑓: 0.29 ( 358 hom. )

Failed GnomAD Quality Control

Consequence

DNAH7
NM_018897.3 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.179

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 -10 ACMG points.

BP6

Variant 2-195897767-TA-T is Benign according to our data. Variant chr2-195897767-TA-T is described in ClinVar as [Benign]. Clinvar id is 402752.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-195897767-TA-T is described in Lovd as [Likely_benign]. Variant chr2-195897767-TA-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 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.4549-3delT		splice_region_variant, intron_variant		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.4549-3delT		splice_region_variant, intron_variant		1	NM_018897.3	ENSP00000311273.6		Q8WXX0-1
DNAH7	ENST00000475293.1 linkuse as main transcript	n.5482-3delT		splice_region_variant, intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

36335

AN:

124844

Hom.:

6361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.535

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.0103

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.211

Gnomad NFE

AF:

0.204

Gnomad OTH

AF:

0.286

GnomAD3 exomes

AF:

0.369

AC:

34356

AN:

93048

Hom.:

AF XY:

0.369

AC XY:

18653

AN XY:

50580

show subpopulations

Gnomad AFR exome

AF:

0.409

Gnomad AMR exome

AF:

0.332

Gnomad ASJ exome

AF:

0.373

Gnomad EAS exome

AF:

0.320

Gnomad SAS exome

AF:

0.360

Gnomad FIN exome

AF:

0.364

Gnomad NFE exome

AF:

0.382

Gnomad OTH exome

AF:

0.348

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.294

AC:

290269

AN:

988694

Hom.:

358

Cov.:

AF XY:

0.294

AC XY:

146773

AN XY:

498868

show subpopulations

Gnomad4 AFR exome

AF:

0.402

Gnomad4 AMR exome

AF:

0.283

Gnomad4 ASJ exome

AF:

0.310

Gnomad4 EAS exome

AF:

0.249

Gnomad4 SAS exome

AF:

0.261

Gnomad4 FIN exome

AF:

0.288

Gnomad4 NFE exome

AF:

0.294

Gnomad4 OTH exome

AF:

0.299

GnomAD4 genome

AF:

0.291

AC:

36367

AN:

124856

Hom.:

6370

Cov.:

AF XY:

0.285

AC XY:

17057

AN XY:

59806

show subpopulations

Gnomad4 AFR

AF:

0.535

Gnomad4 AMR

AF:

0.195

Gnomad4 ASJ

AF:

0.234

Gnomad4 EAS

AF:

0.0106

Gnomad4 SAS

AF:

0.132

Gnomad4 FIN

AF:

0.150

Gnomad4 NFE

AF:

0.204

Gnomad4 OTH

AF:

0.289

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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