NM_018981.4:c.987+1708A>G

Variant names:

• chr2-182738094-A-G
• rs288259
• NM_018981.4:c.987+1708A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018981.4(DNAJC10):​c.987+1708A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,026 control chromosomes in the GnomAD database, including 35,165 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 0.67 (35165 hom., cov: 31)
• Consequence: DNAJC10 NM_018981.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 3 publications found

Genes affected

DNAJC10 (HGNC:24637): (DnaJ heat shock protein family (Hsp40) member C10) This gene encodes an endoplasmic reticulum co-chaperone which is part of the endoplasmic reticulum-associated degradation complex involved in recognizing and degrading misfolded proteins. The encoded protein reduces incorrect disulfide bonds in misfolded glycoproteins. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC10	NM_018981.4	c.987+1708A>G		intron_variant	Intron 11 of 23	ENST00000264065.12	NP_061854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC10	ENST00000264065.12	c.987+1708A>G		intron_variant	Intron 11 of 23	1	NM_018981.4	ENSP00000264065.6

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102259 AN: 151908 Hom.: 35130 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.673 AC: 102341 AN: 152026 Hom.: 35165 Cov.: 31 AF XY: 0.669 AC XY: 49721 AN XY: 74316

African (AFR) AF: 0.800 AC: 33187 AN: 41474

American (AMR) AF: 0.576 AC: 8786 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2707 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2598 AN: 5162

South Asian (SAS) AF: 0.652 AC: 3146 AN: 4822

European-Finnish (FIN) AF: 0.624 AC: 6597 AN: 10568

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.634 AC: 43115 AN: 67952

Other (OTH) AF: 0.696 AC: 1472 AN: 2116

Alfa AF: 0.645 Hom.: 37719

Bravo AF: 0.670

Asia WGS AF: 0.598 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.79
Mutation Taster		=100/0	polymorphism (auto)

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: rs288259; hg19: chr2-183602821;