Variant rs8891 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032317.3(DNAJC30):c.*80A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 1,495,060 control chromosomes in the GnomAD database, including 134,048 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 10696 hom., cov: 31)

Exomes 𝑓: 0.42 ( 123352 hom. )

Consequence

DNAJC30
NM_032317.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.218

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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	UniProt
DNAJC30	NM_032317.3 linkuse as main transcript	c.*80A>G		3_prime_UTR_variant	1/1	ENST00000395176.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJC30	ENST00000395176.3 linkuse as main transcript	c.*80A>G		3_prime_UTR_variant	1/1		NM_032317.3	P1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54651

AN:

151822

Hom.:

10697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.440

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.464

Gnomad EAS

AF:

0.353

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.389

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.383

GnomAD4 exome

AF:

0.425

AC:

570502

AN:

1343120

Hom.:

123352

Cov.:

AF XY:

0.423

AC XY:

278562

AN XY:

658566

show subpopulations

Gnomad4 AFR exome

AF:

0.210

Gnomad4 AMR exome

AF:

0.287

Gnomad4 ASJ exome

AF:

0.451

Gnomad4 EAS exome

AF:

0.309

Gnomad4 SAS exome

AF:

0.339

Gnomad4 FIN exome

AF:

0.397

Gnomad4 NFE exome

AF:

0.446

Gnomad4 OTH exome

AF:

0.413

GnomAD4 genome

AF:

0.360

AC:

54658

AN:

151940

Hom.:

10696

Cov.:

AF XY:

0.356

AC XY:

26462

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.213

Gnomad4 AMR

AF:

0.321

Gnomad4 ASJ

AF:

0.464

Gnomad4 EAS

AF:

0.353

Gnomad4 SAS

AF:

0.332

Gnomad4 FIN

AF:

0.389

Gnomad4 NFE

AF:

0.448

Gnomad4 OTH

AF:

0.380

Alfa

AF:

0.432

Hom.:

15716

Bravo

AF:

0.349

Asia WGS

AF:

0.300

AC:

1043

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

7.9

DANN

Benign

0.28

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over