10-67797487-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_021800.3(DNAJC12):c.503-277T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,094 control chromosomes in the GnomAD database, including 2,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.16 (2242 hom., cov: 32)
• Consequence: DNAJC12 NM_021800.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.42

Genes affected

DNAJC12 (HGNC:28908): (DnaJ heat shock protein family (Hsp40) member C12) This gene encodes a member of a subclass of the HSP40/DnaJ protein family. Members of this family of proteins are associated with complex assembly, protein folding, and export. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 10-67797487-A-G is Benign according to our data. Variant chr10-67797487-A-G is described in ClinVar as [Benign]. Clinvar id is 1291651.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAJC12	NM_021800.3	c.503-277T>C		intron_variant		ENST00000225171.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJC12	ENST00000225171.7	c.503-277T>C		intron_variant		1	NM_021800.3	P1
DNAJC12	ENST00000483798.6	c.593-277T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24935 AN: 151976 Hom.: 2240 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.143

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.164 AC: 24942 AN: 152094 Hom.: 2242 Cov.: 32 AF XY: 0.157 AC XY: 11698 AN XY: 74346

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.0766

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.141

Alfa AF: 0.161 Hom.: 1002

Bravo AF: 0.164

Asia WGS AF: 0.0790 AC: 273 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 29, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.5
Dann	Benign	0.43

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

Other links and lift over

dbSNP: rs7101093; hg19: chr10-69557245;