rs4665736

Variant names:

• chr2-24964730-C-T
• rs4665736
• NM_016544.3:c.171-1256G>A

Variant summary

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

The NM_016544.3(DNAJC27):​c.171-1256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,074 control chromosomes in the GnomAD database, including 16,925 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 0.43 (16925 hom., cov: 32)
• Consequence: DNAJC27 NM_016544.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 56 publications found

Genes affected

DNAJC27 (HGNC:30290): (DnaJ heat shock protein family (Hsp40) member C27) Predicted to enable GTPase activity. Predicted to be involved in intracellular protein transport and positive regulation of MAPK cascade. Predicted to be located in nucleus. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016544.3. 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
	DNAJC27	NM_016544.3	MANE Select	c.171-1256G>A		intron	N/A	NP_057628.1	Q9NZQ0-1
	DNAJC27	NM_001198559.1		c.171-1256G>A		intron	N/A	NP_001185488.1	Q9NZQ0-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC27	ENST00000264711.7	TSL:1 MANE Select	c.171-1256G>A		intron	N/A	ENSP00000264711.2	Q9NZQ0-1
	DNAJC27	ENST00000534855.5	TSL:1	c.171-1256G>A		intron	N/A	ENSP00000440086.2	Q9NZQ0-3
	DNAJC27	ENST00000380809.7	TSL:2	n.171-1256G>A		intron	N/A	ENSP00000370187.3	Q9NZQ0-2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65180 AN: 151956 Hom.: 16910 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.429 AC: 65188 AN: 152074 Hom.: 16925 Cov.: 32 AF XY: 0.440 AC XY: 32697 AN XY: 74348

African (AFR) AF: 0.125 AC: 5173 AN: 41496

American (AMR) AF: 0.588 AC: 8979 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2034 AN: 3464

East Asian (EAS) AF: 0.515 AC: 2670 AN: 5180

South Asian (SAS) AF: 0.510 AC: 2457 AN: 4818

European-Finnish (FIN) AF: 0.614 AC: 6483 AN: 10556

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35710 AN: 67970

Other (OTH) AF: 0.474 AC: 1002 AN: 2112

Alfa AF: 0.501 Hom.: 63774

Bravo AF: 0.414

Asia WGS AF: 0.530 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	10
DANN	Benign	0.66
PhyloP100		0.38
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: rs4665736; hg19: chr2-25187599;