10-21926931-T-A

Variant names:

• chr10-21926931-T-A
• rs2807982
• NM_022365.4:c.371+1575A>T

Variant summary

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

The NM_022365.4(DNAJC1):​c.371+1575A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,014 control chromosomes in the GnomAD database, including 31,595 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 0.64 (31595 hom., cov: 33)
• Consequence: DNAJC1 NM_022365.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 6 publications found

Genes affected

DNAJC1 (HGNC:20090): (DnaJ heat shock protein family (Hsp40) member C1) The membrane protein encoded by this gene is a DNAJ-like heat shock protein that binds the molecular chaperone BiP. In addition, the encoded protein contains two SANT domains that have been shown to bind serpin alpha1-antichymotrypsin and inter-alpha trypsin inhibitor heavy chain 4. [provided by RefSeq, Jul 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022365.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC1	NM_022365.4	MANE Select	c.371+1575A>T		intron	N/A	NP_071760.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC1	ENST00000376980.8	TSL:1 MANE Select	c.371+1575A>T		intron	N/A	ENSP00000366179.3
	DNAJC1	ENST00000376946.2	TSL:3	n.659+2109A>T		intron	N/A
	DNAJC1	ENST00000447548.5	TSL:5	n.336+1575A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97052 AN: 151896 Hom.: 31577 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.639 AC: 97116 AN: 152014 Hom.: 31595 Cov.: 33 AF XY: 0.641 AC XY: 47646 AN XY: 74322

African (AFR) AF: 0.548 AC: 22712 AN: 41456

American (AMR) AF: 0.626 AC: 9558 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3470

East Asian (EAS) AF: 0.955 AC: 4947 AN: 5182

South Asian (SAS) AF: 0.749 AC: 3612 AN: 4824

European-Finnish (FIN) AF: 0.683 AC: 7198 AN: 10538

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45564 AN: 67966

Other (OTH) AF: 0.608 AC: 1285 AN: 2112

Alfa AF: 0.551 Hom.: 1606

Bravo AF: 0.631

Asia WGS AF: 0.784 AC: 2723 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.4
DANN	Benign	0.44
PhyloP100		-0.74
Mutation Taster		=99/1	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: rs2807982; hg19: chr10-22215860;