rs12124078

Variant names:

• chr1-15543404-A-G
• rs12124078
• NM_015291.4:c.575-995A>G

Variant summary

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

The NM_015291.4(DNAJC16):​c.575-995A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,124 control chromosomes in the GnomAD database, including 8,038 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 0.32 (8038 hom., cov: 33)
• Consequence: DNAJC16 NM_015291.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 19 publications found

Genes affected

DNAJC16 (HGNC:29157): (DnaJ heat shock protein family (Hsp40) member C16) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC16	NM_015291.4	c.575-995A>G		intron_variant	Intron 4 of 14	ENST00000375847.8	NP_056106.1
DNAJC16	NM_001287811.2	c.-362-995A>G		intron_variant	Intron 3 of 13		NP_001274740.1
DNAJC16	NR_109898.2	n.704-995A>G		intron_variant	Intron 4 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC16	ENST00000375847.8	c.575-995A>G		intron_variant	Intron 4 of 14	1	NM_015291.4	ENSP00000365007.3

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48251 AN: 152006 Hom.: 8028 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.317 AC: 48277 AN: 152124 Hom.: 8038 Cov.: 33 AF XY: 0.320 AC XY: 23792 AN XY: 74358

African (AFR) AF: 0.305 AC: 12662 AN: 41494

American (AMR) AF: 0.310 AC: 4750 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3472

East Asian (EAS) AF: 0.582 AC: 3006 AN: 5164

South Asian (SAS) AF: 0.244 AC: 1178 AN: 4826

European-Finnish (FIN) AF: 0.368 AC: 3887 AN: 10564

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20945 AN: 67988

Other (OTH) AF: 0.291 AC: 615 AN: 2112

Alfa AF: 0.315 Hom.: 10870

Bravo AF: 0.314

Asia WGS AF: 0.396 AC: 1378 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	0.92
DANN	Benign	0.26
PhyloP100		-0.27
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: rs12124078; hg19: chr1-15869899;