dbSNP rs4850381: DNAH7:c.398+9T>C (chr2-196047343-A-G) – 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_018897.3(DNAH7):c.398+9T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 1,559,550 control chromosomes in the GnomAD database, including 411,974 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.73 ( 40771 hom., cov: 31)

Exomes 𝑓: 0.72 ( 371203 hom. )

Consequence

DNAH7
NM_018897.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.768

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:

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=-0.86).

BP6

Variant 2-196047343-A-G is Benign according to our data. Variant chr2-196047343-A-G is described in ClinVar as [Benign]. Clinvar id is 402757.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH7	NM_018897.3 link	c.398+9T>C		intron_variant	Intron 5 of 64	ENST00000312428.11	NP_061720.2	Q8WXX0-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAH7	ENST00000312428.11 link	c.398+9T>C	intron_variant	Intron 5 of 64	1	NM_018897.3	ENSP00000311273.6	Q8WXX0-1
DNAH7	ENST00000410072.5 link	c.398+9T>C	intron_variant	Intron 5 of 12	2		ENSP00000386260.1	Q8WXX0-4
DNAH7	ENST00000427816.1 link	c.323+9T>C	intron_variant	Intron 5 of 5	4		ENSP00000407444.1	C9JUY3

Frequencies

GnomAD3 genomes

AF:

0.731

AC:

111014

AN:

151952

Hom.:

40714

Cov.:

show subpopulations

Gnomad AFR

AF:

0.745

Gnomad AMI

AF:

0.734

Gnomad AMR

AF:

0.741

Gnomad ASJ

AF:

0.615

Gnomad EAS

AF:

0.904

Gnomad SAS

AF:

0.703

Gnomad FIN

AF:

0.730

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.716

Gnomad OTH

AF:

0.711

GnomAD3 exomes

AF:

0.734

AC:

169040

AN:

230366

Hom.:

62603

AF XY:

0.727

AC XY:

91184

AN XY:

125490

show subpopulations

Gnomad AFR exome

AF:

0.738

Gnomad AMR exome

AF:

0.793

Gnomad ASJ exome

AF:

0.621

Gnomad EAS exome

AF:

0.903

Gnomad SAS exome

AF:

0.692

Gnomad FIN exome

AF:

0.735

Gnomad NFE exome

AF:

0.713

Gnomad OTH exome

AF:

0.707

GnomAD4 exome

AF:

0.724

AC:

1019497

AN:

1407480

Hom.:

371203

Cov.:

AF XY:

0.721

AC XY:

503865

AN XY:

698366

show subpopulations

Gnomad4 AFR exome

AF:

0.745

Gnomad4 AMR exome

AF:

0.785

Gnomad4 ASJ exome

AF:

0.623

Gnomad4 EAS exome

AF:

0.919

Gnomad4 SAS exome

AF:

0.693

Gnomad4 FIN exome

AF:

0.737

Gnomad4 NFE exome

AF:

0.720

Gnomad4 OTH exome

AF:

0.719

GnomAD4 genome

AF:

0.731

AC:

111130

AN:

152070

Hom.:

40771

Cov.:

AF XY:

0.732

AC XY:

54399

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.745

Gnomad4 AMR

AF:

0.741

Gnomad4 ASJ

AF:

0.615

Gnomad4 EAS

AF:

0.904

Gnomad4 SAS

AF:

0.703

Gnomad4 FIN

AF:

0.730

Gnomad4 NFE

AF:

0.716

Gnomad4 OTH

AF:

0.712

Alfa

AF:

0.712

Hom.:

89550

Bravo

AF:

0.733

Asia WGS

AF:

0.792

AC:

2755

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

Mar 29, 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

-0.86

CADD

Benign

0.18

DANN

Benign

0.35

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