rs7894262

Variant names:

• chr10-72335295-G-A
• rs7894262
• NM_017626.7:c.*30+485C>T

Variant summary

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

The NM_001002762.5(DNAJB12):​c.*515C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0471 in 987,580 control chromosomes in the GnomAD database, including 3,564 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 0.12 (2347 hom., cov: 33)
  • Exomes 𝑓: 0.034 (1217 hom.)
• Consequence: DNAJB12 NM_001002762.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 1 publications found

Genes affected

DNAJB12 (HGNC:14891): (DnaJ heat shock protein family (Hsp40) member B12) DNAJB12 belongs to the evolutionarily conserved DNAJ/HSP40 family of proteins, which regulate molecular chaperone activity by stimulating ATPase activity. DNAJ proteins may have up to 3 distinct domains: a conserved 70-amino acid J domain, usually at the N terminus; a glycine/phenylalanine (G/F)-rich region; and a cysteine-rich domain containing 4 motifs resembling a zinc finger domain (Ohtsuka and Hata, 2000 [PubMed 11147971]).[supplied by OMIM, Mar 2008]

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 = 0.318 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002762.5. 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
	DNAJB12	NM_017626.7	MANE Select	c.*30+485C>T		intron	N/A	NP_060096.4
	DNAJB12	NM_001002762.5		c.*515C>T		3_prime_UTR	Exon 8 of 8	NP_001002762.3	Q9NXW2-1
	DNAJB12	NM_001365080.3		c.1104+539C>T		intron	N/A	NP_001352009.1	Q9NXW2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJB12	ENST00000444643.8	TSL:1 MANE Select	c.*30+485C>T		intron	N/A	ENSP00000403313.2	Q9NXW2-1
	DNAJB12	ENST00000394903.6	TSL:1	c.*30+485C>T		intron	N/A	ENSP00000378363.2	J3KPS0
	DNAJB12	ENST00000338820.7	TSL:2	c.*515C>T		3_prime_UTR	Exon 8 of 8	ENSP00000345575.3	J3KPS0

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17704 AN: 152128 Hom.: 2325 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0683

Gnomad FIN AF: 0.0213

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0961

GnomAD4 exome AF: 0.0344 AC: 28769 AN: 835334 Hom.: 1217 Cov.: 32 AF XY: 0.0337 AC XY: 13020 AN XY: 385992

African (AFR) AF: 0.329 AC: 5199 AN: 15804

American (AMR) AF: 0.0492 AC: 58 AN: 1178

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 120 AN: 5186

East Asian (EAS) AF: 0.130 AC: 473 AN: 3652

South Asian (SAS) AF: 0.0608 AC: 1029 AN: 16936

European-Finnish (FIN) AF: 0.0206 AC: 9 AN: 436

Middle Eastern (MID) AF: 0.0623 AC: 101 AN: 1620

European-Non Finnish (NFE) AF: 0.0267 AC: 20341 AN: 763150

Other (OTH) AF: 0.0526 AC: 1439 AN: 27372

GnomAD4 genome AF: 0.117 AC: 17768 AN: 152246 Hom.: 2347 Cov.: 33 AF XY: 0.114 AC XY: 8508 AN XY: 74444

African (AFR) AF: 0.323 AC: 13409 AN: 41522

American (AMR) AF: 0.0592 AC: 905 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3472

East Asian (EAS) AF: 0.121 AC: 625 AN: 5172

South Asian (SAS) AF: 0.0677 AC: 327 AN: 4828

European-Finnish (FIN) AF: 0.0213 AC: 226 AN: 10616

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0282 AC: 1919 AN: 68016

Other (OTH) AF: 0.0956 AC: 202 AN: 2114

Alfa AF: 0.0782 Hom.: 175

Bravo AF: 0.130

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.60
DANN	Benign	0.61
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7894262;

hg19: chr10-74095053;