rs1043615

Variant names:

• chr7-108571909-G-A
• rs1043615
• NM_012328.3:c.183G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-108571909-G-A
• chr7-108571909-G-C
• chr7-108571909-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_012328.3(DNAJB9):​c.183G>A​(p.Pro61Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 1,613,686 control chromosomes in the GnomAD database, including 218,132 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 0.46 (17286 hom., cov: 32)
  • Exomes 𝑓: 0.52 (200846 hom.)
• Consequence: DNAJB9 NM_012328.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 27 publications found

Genes affected

DNAJB9 (HGNC:6968): (DnaJ heat shock protein family (Hsp40) member B9) 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. This gene is a member of the type 2 subgroup of DnaJ proteins. The encoded protein is localized to the endoplasmic reticulum. This protein is induced by endoplasmic reticulum stress and plays a role in protecting stressed cells from apoptosis. [provided by RefSeq, Dec 2010]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BP7: Synonymous conserved (PhyloP=0.206 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012328.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJB9	NM_012328.3	MANE Select	c.183G>A	p.Pro61Pro	synonymous	Exon 2 of 3	NP_036460.1	Q6FIF1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJB9	ENST00000249356.4	TSL:1 MANE Select	c.183G>A	p.Pro61Pro	synonymous	Exon 2 of 3	ENSP00000249356.3	Q9UBS3
	DNAJB9	ENST00000860473.1		c.183G>A	p.Pro61Pro	synonymous	Exon 2 of 3	ENSP00000530532.1
	DNAJB9	ENST00000860474.1		c.183G>A	p.Pro61Pro	synonymous	Exon 1 of 2	ENSP00000530533.1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70540 AN: 151838 Hom.: 17275 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.459

GnomAD2 exomes AF: 0.523 AC: 131515 AN: 251372 AF XY: 0.522

Gnomad AFR exome AF: 0.299

Gnomad AMR exome AF: 0.629

Gnomad ASJ exome AF: 0.425

Gnomad EAS exome AF: 0.613

Gnomad FIN exome AF: 0.534

Gnomad NFE exome AF: 0.515

Gnomad OTH exome AF: 0.515

GnomAD4 exome AF: 0.522 AC: 762859 AN: 1461730 Hom.: 200846 Cov.: 57 AF XY: 0.522 AC XY: 379451 AN XY: 727168

African (AFR) AF: 0.292 AC: 9784 AN: 33474

American (AMR) AF: 0.618 AC: 27624 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 11226 AN: 26130

East Asian (EAS) AF: 0.601 AC: 23844 AN: 39688

South Asian (SAS) AF: 0.522 AC: 45048 AN: 86254

European-Finnish (FIN) AF: 0.531 AC: 28344 AN: 53406

Middle Eastern (MID) AF: 0.437 AC: 2522 AN: 5768

European-Non Finnish (NFE) AF: 0.525 AC: 583704 AN: 1111898

Other (OTH) AF: 0.509 AC: 30763 AN: 60390

GnomAD4 genome AF: 0.464 AC: 70568 AN: 151956 Hom.: 17286 Cov.: 32 AF XY: 0.470 AC XY: 34928 AN XY: 74270

African (AFR) AF: 0.300 AC: 12443 AN: 41436

American (AMR) AF: 0.566 AC: 8634 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1465 AN: 3462

East Asian (EAS) AF: 0.598 AC: 3085 AN: 5156

South Asian (SAS) AF: 0.506 AC: 2441 AN: 4820

European-Finnish (FIN) AF: 0.546 AC: 5775 AN: 10568

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35255 AN: 67946

Other (OTH) AF: 0.453 AC: 952 AN: 2102

Alfa AF: 0.497 Hom.: 78907

Bravo AF: 0.458

Asia WGS AF: 0.484 AC: 1686 AN: 3478

EpiCase AF: 0.509

EpiControl AF: 0.503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	7.7
DANN	Benign	0.82
PhyloP100		0.21
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
Mutation Taster		=92/8	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: rs1043615; hg19: chr7-108212353; COSMIC: COSV50812154; COSMIC: COSV50812154;