Genetic Variant DNAJC11:c.*612G>A (chr1-6635063-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018198.4(DNAJC11):c.*612G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 231,772 control chromosomes in the GnomAD database, including 54,413 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 0.68 ( 35796 hom., cov: 32)

Exomes 𝑓: 0.68 ( 18617 hom. )

Consequence

DNAJC11
NM_018198.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.148

Variant links:

Genes affected

DNAJC11 (HGNC:25570): (DnaJ heat shock protein family (Hsp40) member C11) Involved in cristae formation. Located in mitochondrial outer membrane and nuclear speck. Part of MIB complex. Colocalizes with MICOS complex and SAM complex. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC11 links:

THAP3 (HGNC:20855): (THAP domain containing 3) Predicted to enable DNA binding activity and metal ion binding activity. Involved in positive regulation of transcription by RNA polymerase II. [provided by Alliance of Genome Resources, Apr 2022]

THAP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC11	NM_018198.4 link	c.*612G>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000377577.10	NP_060668.2	Q9NVH1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC11	ENST00000377577 link	c.*612G>A		3_prime_UTR_variant	Exon 16 of 16	1	NM_018198.4	ENSP00000366800.5		Q9NVH1-1

Frequencies

GnomAD3 genomes

AF:

0.683

AC:

103778

AN:

151964

Hom.:

35759

Cov.:

show subpopulations

Gnomad AFR

AF:

0.720

Gnomad AMI

AF:

0.591

Gnomad AMR

AF:

0.601

Gnomad ASJ

AF:

0.749

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.765

Gnomad FIN

AF:

0.597

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.690

Gnomad OTH

AF:

0.715

GnomAD4 exome

AF:

0.677

AC:

53936

AN:

79690

Hom.:

18617

Cov.:

AF XY:

0.679

AC XY:

27839

AN XY:

40974

show subpopulations

Gnomad4 AFR exome

AF:

0.710

Gnomad4 AMR exome

AF:

0.532

Gnomad4 ASJ exome

AF:

0.758

Gnomad4 EAS exome

AF:

0.601

Gnomad4 SAS exome

AF:

0.740

Gnomad4 FIN exome

AF:

0.597

Gnomad4 NFE exome

AF:

0.685

Gnomad4 OTH exome

AF:

0.688

GnomAD4 genome

AF:

0.683

AC:

103869

AN:

152082

Hom.:

35796

Cov.:

AF XY:

0.680

AC XY:

50583

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.720

Gnomad4 AMR

AF:

0.600

Gnomad4 ASJ

AF:

0.749

Gnomad4 EAS

AF:

0.589

Gnomad4 SAS

AF:

0.766

Gnomad4 FIN

AF:

0.597

Gnomad4 NFE

AF:

0.690

Gnomad4 OTH

AF:

0.716

Alfa

AF:

0.695

Hom.:

61876

Bravo

AF:

0.680

Asia WGS

AF:

0.673

AC:

2344

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.4

DANN

Benign

0.78

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