Genetic Variant NM_018897.3:c.11555A>G (chr2-195756164-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_018897.3(DNAH7):c.11555A>G(p.Asn3852Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00306 in 1,607,940 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.017 ( 68 hom., cov: 32)

Exomes 𝑓: 0.0016 ( 63 hom. )

Consequence

DNAH7
NM_018897.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0180

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:

LOC107985972 (HGNC:):

LOC107985972 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 (MetaRNN=0.0032253861).

BP6

Variant 2-195756164-T-C is Benign according to our data. Variant chr2-195756164-T-C is described in ClinVar as [Benign]. Clinvar id is 709627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH7	NM_018897.3 link	c.11555A>G	p.Asn3852Ser	missense_variant	Exon 62 of 65	ENST00000312428.11	NP_061720.2	Q8WXX0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAH7	ENST00000312428.11 link	c.11555A>G	p.Asn3852Ser	missense_variant	Exon 62 of 65	1	NM_018897.3	ENSP00000311273.6	Q8WXX0-1
DNAH7	ENST00000409063.5 link	c.1004A>G	p.Asn335Ser	missense_variant	Exon 7 of 10	1		ENSP00000386912.1	Q8WXX0-2
DNAH7	ENST00000438565.1 link	c.35A>G	p.Asn12Ser	missense_variant	Exon 1 of 3	3		ENSP00000409732.1	H7C362

Frequencies

GnomAD3 genomes

AF:

0.0168

AC:

2549

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0578

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00752

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.000147

Gnomad OTH

AF:

0.0124

GnomAD3 exomes

AF:

0.00427

AC:

1053

AN:

246356

Hom.:

AF XY:

0.00344

AC XY:

460

AN XY:

133672

show subpopulations

Gnomad AFR exome

AF:

0.0587

Gnomad AMR exome

AF:

0.00314

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000168

Gnomad FIN exome

AF:

0.000233

Gnomad NFE exome

AF:

0.000134

Gnomad OTH exome

AF:

0.00285

GnomAD4 exome

AF:

0.00163

AC:

2368

AN:

1455646

Hom.:

Cov.:

AF XY:

0.00139

AC XY:

1009

AN XY:

723336

show subpopulations

Gnomad4 AFR exome

AF:

0.0569

Gnomad4 AMR exome

AF:

0.00336

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000176

Gnomad4 FIN exome

AF:

0.000394

Gnomad4 NFE exome

AF:

0.0000460

Gnomad4 OTH exome

AF:

0.00374

GnomAD4 genome

AF:

0.0168

AC:

2553

AN:

152294

Hom.:

Cov.:

AF XY:

0.0167

AC XY:

1244

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0577

Gnomad4 AMR

AF:

0.00751

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.000147

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.00286

Hom.:

Bravo

AF:

0.0184

ESP6500AA

AF:

0.0567

AC:

208

ESP6500EA

AF:

0.000122

AC:

ExAC

AF:

0.00537

AC:

649

Asia WGS

AF:

0.00260

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

AlphaMissense

Benign

0.067

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.79

DEOGEN2

Benign

0.012

.;T;.

Eigen

Benign

-0.33

Eigen_PC

Benign

-0.11

FATHMM_MKL

Benign

0.75

LIST_S2

Uncertain

0.90

D;D;D

MetaRNN

Benign

0.0032

T;T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

0.64

.;N;.

PrimateAI

Uncertain

0.52

PROVEAN

Uncertain

-3.6

D;N;D

REVEL

Benign

0.12

Sift

Benign

0.75

T;T;.

Sift4G

Benign

0.48

T;.;.

Polyphen

0.020

.;B;.

Vest4

0.13

MVP

0.14

MPC

0.030

ClinPred

0.018

GERP RS

5.2

Varity_R

0.14

gMVP

0.25

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