2-24964730-C-T

Position:

• chr2-24964730-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC27	NM_016544.3	c.171-1256G>A		intron_variant		ENST00000264711.7	NP_057628.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC27	ENST00000264711.7	c.171-1256G>A		intron_variant		1	NM_016544.3	ENSP00000264711	P1

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.474

Alfa AF: 0.522 Hom.: 27650

Bravo AF: 0.414

Asia WGS AF: 0.530 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	10
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs4665736; hg19: chr2-25187599;