11-64232057-C-G

Variant names:

• chr11-64232057-C-G
• rs3741403
• NM_005528.4:c.180+93C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005528.4(DNAJC4):​c.180+93C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000169 in 1,183,604 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000017 (0 hom.)
• Consequence: DNAJC4 NM_005528.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 22 publications found

Genes affected

DNAJC4 (HGNC:5271): (DnaJ heat shock protein family (Hsp40) member C4) Predicted to be involved in response to unfolded protein. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000256116 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC4	NM_005528.4	c.180+93C>G		intron_variant	Intron 2 of 5	ENST00000628077.3	NP_005519.2
DNAJC4	NM_001307980.1	c.180+93C>G		intron_variant	Intron 2 of 4		NP_001294909.1
DNAJC4	NM_001307981.1	c.180+93C>G		intron_variant	Intron 2 of 4		NP_001294910.1
DNAJC4	XM_047426865.1	c.180+93C>G		intron_variant	Intron 2 of 5		XP_047282821.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC4	ENST00000628077.3	c.180+93C>G		intron_variant	Intron 2 of 5	5	NM_005528.4	ENSP00000486499.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000169 AC: 2 AN: 1183604 Hom.: 0 Cov.: 16 AF XY: 0.00000167 AC XY: 1 AN XY: 598850

African (AFR) AF: 0.00 AC: 0 AN: 27972

American (AMR) AF: 0.00 AC: 0 AN: 40148

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23812

East Asian (EAS) AF: 0.00 AC: 0 AN: 37984

South Asian (SAS) AF: 0.0000127 AC: 1 AN: 78806

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44694

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5262

European-Non Finnish (NFE) AF: 0.00000114 AC: 1 AN: 873486

Other (OTH) AF: 0.00 AC: 0 AN: 51440

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 24139

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.65
PhyloP100		-1.2
PromoterAI		0.020	Neutral

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

Other links and lift over

dbSNP: rs3741403; hg19: chr11-63999529;