ENST00000360864:c.-35_-20delGCGGGCGGGCGGGCGG

Variant names:

• chr20-63895297-AGGGCGGGCGGGCGGGC-A
• rs917983556
• ENST00000360864:c.-35_-20delGCGGGCGGGCGGGCGG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000360864(DNAJC5):​c.-35_-20delGCGGGCGGGCGGGCGG variant causes a 5 prime UTR 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: 32)
• Consequence: DNAJC5 ENST00000360864 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23

Genes affected

DNAJC5 (HGNC:16235): (DnaJ heat shock protein family (Hsp40) member C5) This gene is a member of the J protein family. J proteins function in many cellular processes by regulating the ATPase activity of 70 kDa heat shock proteins. The encoded protein plays a role in membrane trafficking and protein folding, and has been shown to have anti-neurodegenerative properties. The encoded protein is known to play a role in cystic fibrosis and Huntington's disease. A pseudogene of this gene is located on the short arm of chromosome 8. [provided by RefSeq, Nov 2010]

ENSG00000290226 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 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
DNAJC5	NM_025219.3	c.-35_-20delGCGGGCGGGCGGGCGG		5_prime_UTR_variant	Exon 1 of 5	ENST00000360864.9	NP_079495.1
DNAJC5	XM_047440509.1	c.-1720_-1705delGCGGGCGGGCGGGCGG		5_prime_UTR_variant	Exon 1 of 5		XP_047296465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC5	ENST00000360864	c.-35_-20delGCGGGCGGGCGGGCGG		5_prime_UTR_variant	Exon 1 of 5	1	NM_025219.3	ENSP00000354111.4
DNAJC5	ENST00000470551.1	n.-35_-20delGCGGGCGGGCGGGCGG		non_coding_transcript_exon_variant	Exon 1 of 6	2		ENSP00000434744.1
DNAJC5	ENST00000470551.1	n.-35_-20delGCGGGCGGGCGGGCGG		5_prime_UTR_variant	Exon 1 of 6	2		ENSP00000434744.1
ENSG00000290226	ENST00000703636.1	n.453+12480_453+12495delGCGGGCGGGCGGGCGG		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs917983556; hg19: chr20-62526650;