15-40783204-C-T

Variant names:

• chr15-40783204-C-T
• rs3092985
• NM_018163.3:c.79-3207G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018163.3(DNAJC17):​c.79-3207G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,040 control chromosomes in the GnomAD database, including 24,455 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 0.56 (24455 hom., cov: 32)
• Consequence: DNAJC17 NM_018163.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

DNAJC17 (HGNC:25556): (DnaJ heat shock protein family (Hsp40) member C17) Predicted to enable RNA binding activity. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II and toxin transport. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC17	NM_018163.3	c.79-3207G>A		intron_variant	Intron 1 of 10	ENST00000220496.9	NP_060633.1
DNAJC17	XM_047432788.1	c.79-3207G>A		intron_variant	Intron 1 of 8		XP_047288744.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC17	ENST00000220496.9	c.79-3207G>A		intron_variant	Intron 1 of 10	1	NM_018163.3	ENSP00000220496.4

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84338 AN: 151922 Hom.: 24399 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.555 AC: 84455 AN: 152040 Hom.: 24455 Cov.: 32 AF XY: 0.557 AC XY: 41371 AN XY: 74312

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.526

Alfa AF: 0.569 Hom.: 3578

Bravo AF: 0.546

Asia WGS AF: 0.600 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.21

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: rs3092985; hg19: chr15-41075402;