12-49349505-G-T

Position:

• chr12-49349505-G-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001304944.2(DNAJC22):​c.633G>T​(p.Val211Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: DNAJC22 NM_001304944.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.188

Genes affected

DNAJC22 (HGNC:25802): (DnaJ heat shock protein family (Hsp40) member C22) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP6: Variant 12-49349505-G-T is Benign according to our data. Variant chr12-49349505-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3234408.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.188 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC22	NM_001304944.2	c.633G>T	p.Val211Val	synonymous_variant	3/4	ENST00000549441.7	NP_001291873.1
DNAJC22	NM_024902.4	c.633G>T	p.Val211Val	synonymous_variant	2/3		NP_079178.2
DNAJC22	XM_047429555.1	c.633G>T	p.Val211Val	synonymous_variant	3/6		XP_047285511.1
DNAJC22	XM_047429556.1	c.633G>T	p.Val211Val	synonymous_variant	3/5		XP_047285512.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC22	ENST00000549441.7	c.633G>T	p.Val211Val	synonymous_variant	3/4	2	NM_001304944.2	ENSP00000446830.1
DNAJC22	ENST00000395069.3	c.633G>T	p.Val211Val	synonymous_variant	2/3	1		ENSP00000378508.2
DNAJC22	ENST00000647553.1	n.633G>T		non_coding_transcript_exon_variant	2/4			ENSP00000498036.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2024

DNAJC22: PM2:Supporting, BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	3.7
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-49743288; COSMIC: COSV67712670; COSMIC: COSV67712670;