DNAJC16 p.Arg534Arg

Variant names:

• chr1-15565919-G-G
• NM_015291.4:c.

Your query was ambiguous. Multiple possible variants found:

• chr1-15565920--
• chr1-15565920-A-C
• chr1-15565922-G-A
• chr1-15565920-AGG-CGT
• chr1-15565920-AGG-CGC
• chr1-15565920-AGG-CGA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_015291.4(DNAJC16):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: DNAJC16 NM_015291.4 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 0 publications found

Genes affected

DNAJC16 (HGNC:29157): (DnaJ heat shock protein family (Hsp40) member C16) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000272510 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015291.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC16	NM_015291.4	MANE Select	c.		exon_region	Exon 15 of 15	NP_056106.1	Q9Y2G8-1
	DNAJC16	NM_015291.4	MANE Select	c.		3_prime_UTR	Exon 15 of 15	NP_056106.1	Q9Y2G8-1
	DNAJC16	NM_001287811.2		c.		exon_region	Exon 14 of 14	NP_001274740.1	Q9Y2G8-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC16	ENST00000375847.8	TSL:1 MANE Select	c.		splice_region intron	N/A	ENSP00000365007.3	Q9Y2G8-1
	DNAJC16	ENST00000375849.5	TSL:1	c.		splice_region intron	N/A	ENSP00000365009.1	Q5TDH4
	DNAJC16	ENST00000616884.4	TSL:1	c.		splice_region intron	N/A	ENSP00000480224.1	Q9Y2G8-2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-15892414;