Variant chr7-73683324-C-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_032317.3(DNAJC30):c.100G>A(p.Gly34Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 1,613,630 control chromosomes in the GnomAD database, including 143,552 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.36 ( 10687 hom., cov: 34)

Exomes 𝑓: 0.42 ( 132865 hom. )

Consequence

DNAJC30
NM_032317.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.486

Variant links:

Genes affected

DNAJC30 (HGNC:16410): (DnaJ heat shock protein family (Hsp40) member C30) This intronless gene encodes a member of the DNAJ molecular chaperone homology domain-containing protein family. This gene is deleted in Williams syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. [provided by RefSeq, Jul 2008]

DNAJC30 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=4.937053E-4).

BP6

Variant 7-73683324-C-T is Benign according to our data. Variant chr7-73683324-C-T is described in ClinVar as [Benign]. Clinvar id is 1254123.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC30	NM_032317.3 linkuse as main transcript	c.100G>A	p.Gly34Arg	missense_variant	1/1	ENST00000395176.3	NP_115693.2	Q96LL9B3KSU4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC30	ENST00000395176.3 linkuse as main transcript	c.100G>A	p.Gly34Arg	missense_variant	1/1	6	NM_032317.3	ENSP00000378605.1		Q96LL9

Frequencies

GnomAD3 genomes

AF:

0.359

AC:

54664

AN:

152126

Hom.:

10688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.439

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.441

Gnomad EAS

AF:

0.353

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.382

GnomAD3 exomes

AF:

0.383

AC:

94745

AN:

247294

Hom.:

19097

AF XY:

0.389

AC XY:

52405

AN XY:

134608

show subpopulations

Gnomad AFR exome

AF:

0.207

Gnomad AMR exome

AF:

0.269

Gnomad ASJ exome

AF:

0.435

Gnomad EAS exome

AF:

0.365

Gnomad SAS exome

AF:

0.337

Gnomad FIN exome

AF:

0.401

Gnomad NFE exome

AF:

0.449

Gnomad OTH exome

AF:

0.411

GnomAD4 exome

AF:

0.422

AC:

616823

AN:

1461386

Hom.:

132865

Cov.:

102

AF XY:

0.421

AC XY:

305935

AN XY:

726980

show subpopulations

Gnomad4 AFR exome

AF:

0.211

Gnomad4 AMR exome

AF:

0.279

Gnomad4 ASJ exome

AF:

0.433

Gnomad4 EAS exome

AF:

0.309

Gnomad4 SAS exome

AF:

0.342

Gnomad4 FIN exome

AF:

0.399

Gnomad4 NFE exome

AF:

0.445

Gnomad4 OTH exome

AF:

0.411

GnomAD4 genome

AF:

0.359

AC:

54675

AN:

152244

Hom.:

10687

Cov.:

AF XY:

0.356

AC XY:

26505

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.213

Gnomad4 AMR

AF:

0.321

Gnomad4 ASJ

AF:

0.441

Gnomad4 EAS

AF:

0.353

Gnomad4 SAS

AF:

0.332

Gnomad4 FIN

AF:

0.390

Gnomad4 NFE

AF:

0.448

Gnomad4 OTH

AF:

0.379

Alfa

AF:

0.431

Hom.:

29592

Bravo

AF:

0.348

TwinsUK

AF:

0.460

AC:

1706

ALSPAC

AF:

0.455

AC:

1755

ESP6500AA

AF:

0.211

AC:

923

ESP6500EA

AF:

0.448

AC:

3837

ExAC

AF:

0.383

AC:

46416

Asia WGS

AF:

0.298

AC:

1038

AN:

3478

EpiCase

AF:

0.452

EpiControl

AF:

0.449

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 07, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

5.7

DANN

Benign

0.88

DEOGEN2

Benign

0.0018

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.023

LIST_S2

Benign

0.40

MetaRNN

Benign

0.00049

MetaSVM

Benign

-0.97

MutationAssessor

Benign

0.95

PrimateAI

Benign

0.36

PROVEAN

Benign

0.050

REVEL

Benign

0.059

Sift

Benign

0.61

Sift4G

Benign

0.59

Polyphen

0.0

Vest4

0.022

MutPred

0.14

Gain of sheet (P = 0.0507);

MPC

0.47

ClinPred

0.0011

GERP RS

-1.8

Varity_R

0.044

gMVP

0.20

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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