1-15559647-G-C

Variant names:

• chr1-15559647-G-C
• rs772896520
• NM_015291.4:c.1145G>C

Variant summary

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

The NM_015291.4(DNAJC16):​c.1145G>C​(p.Arg382Pro) variant causes a missense change involving the alteration of a 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R382Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DNAJC16 NM_015291.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.25

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]

ACMG classification

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC16	NM_015291.4	c.1145G>C	p.Arg382Pro	missense_variant	Exon 8 of 15	ENST00000375847.8	NP_056106.1
DNAJC16	NM_001287811.2	c.209G>C	p.Arg70Pro	missense_variant	Exon 7 of 14		NP_001274740.1
DNAJC16	NR_109898.2	n.1274G>C		non_coding_transcript_exon_variant	Exon 8 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC16	ENST00000375847.8	c.1145G>C	p.Arg382Pro	missense_variant	Exon 8 of 15	1	NM_015291.4	ENSP00000365007.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.82
BayesDel_addAF	Pathogenic	0.21	D
BayesDel_noAF	Uncertain	0.060
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0021	T;.;T;T
Eigen	Pathogenic	0.78
Eigen_PC	Pathogenic	0.83
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.97	.;D;D;D
M_CAP	Benign	0.014	T
MetaRNN	Uncertain	0.74	D;D;D;D
MetaSVM	Benign	-1.2	T
MutationAssessor	Uncertain	2.3	.;.;M;.
PhyloP100		9.2
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	0.25	N;.;N;N
REVEL	Uncertain	0.30
Sift	Benign	0.23	T;.;T;T
Sift4G	Uncertain	0.0080	D;D;D;D
Polyphen		1.0	D;.;D;.
Vest4		0.81
MutPred		0.46		Loss of MoRF binding (P = 0.0065);.;Loss of MoRF binding (P = 0.0065);Loss of MoRF binding (P = 0.0065);
MVP		0.60
MPC		0.81
ClinPred		0.82	D
GERP RS		6.2
Varity_R		0.24
gMVP		0.78
Mutation Taster		=17/83	disease causing

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

Loading publications...

Other links and lift over

dbSNP: rs772896520; hg19: chr1-15886142;