dbSNP rs139722368: JMJD1C:p.Gly1158_Leu1159del (chr10-63208190-ACTAAAC-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBA1

The NM_032776.3(JMJD1C):c.3473_3478delGTTTAG(p.Gly1158_Leu1159del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0352 in 1,613,900 control chromosomes in the GnomAD database, including 2,327 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.035 ( 277 hom., cov: 32)

Exomes 𝑓: 0.035 ( 2050 hom. )

Consequence

JMJD1C
NM_032776.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 4.51

Variant links:

Genes affected

JMJD1C (HGNC:12313): (jumonji domain containing 1C) The protein encoded by this gene interacts with thyroid hormone receptors and contains a jumonji domain. It is a candidate histone demethylase and is thought to be a coactivator for key transcription factors. It plays a role in the DNA-damage response pathway by demethylating the mediator of DNA damage checkpoint 1 (MDC1) protein, and is required for the survival of acute myeloid leukemia. Mutations in this gene are associated with Rett syndrome and intellectual disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

JMJD1C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_032776.3.

BP6

Variant 10-63208190-ACTAAAC-A is Benign according to our data. Variant chr10-63208190-ACTAAAC-A is described in ClinVar as [Benign]. Clinvar id is 529718.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JMJD1C	NM_032776.3 link	c.3473_3478delGTTTAG	p.Gly1158_Leu1159del	disruptive_inframe_deletion	Exon 10 of 26	ENST00000399262.7	NP_116165.1	Q15652-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
JMJD1C	ENST00000399262.7 link	c.3473_3478delGTTTAG	p.Gly1158_Leu1159del	disruptive_inframe_deletion	Exon 10 of 26	5	NM_032776.3	ENSP00000382204.2	Q15652-1
JMJD1C	ENST00000542921.5 link	c.2927_2932delGTTTAG	p.Gly976_Leu977del	disruptive_inframe_deletion	Exon 9 of 25	1		ENSP00000444682.1	Q15652-3
JMJD1C	ENST00000402544.5 link	n.3445_3450delGTTTAG		non_coding_transcript_exon_variant	Exon 7 of 22	1

Frequencies

GnomAD3 genomes

AF:

0.0349

AC:

5305

AN:

152184

Hom.:

275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00917

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0897

Gnomad ASJ

AF:

0.00979

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.0213

Gnomad FIN

AF:

0.0317

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0245

Gnomad OTH

AF:

0.0267

GnomAD3 exomes

AF:

0.0533

AC:

13273

AN:

248954

Hom.:

1034

AF XY:

0.0482

AC XY:

6516

AN XY:

135062

show subpopulations

Gnomad AFR exome

AF:

0.00898

Gnomad AMR exome

AF:

0.115

Gnomad ASJ exome

AF:

0.0103

Gnomad EAS exome

AF:

0.269

Gnomad SAS exome

AF:

0.0162

Gnomad FIN exome

AF:

0.0322

Gnomad NFE exome

AF:

0.0247

Gnomad OTH exome

AF:

0.0393

GnomAD4 exome

AF:

0.0353

AC:

51559

AN:

1461598

Hom.:

2050

AF XY:

0.0340

AC XY:

24705

AN XY:

727110

show subpopulations

Gnomad4 AFR exome

AF:

0.00636

Gnomad4 AMR exome

AF:

0.112

Gnomad4 ASJ exome

AF:

0.00922

Gnomad4 EAS exome

AF:

0.227

Gnomad4 SAS exome

AF:

0.0167

Gnomad4 FIN exome

AF:

0.0326

Gnomad4 NFE exome

AF:

0.0282

Gnomad4 OTH exome

AF:

0.0420

GnomAD4 genome

AF:

0.0349

AC:

5308

AN:

152302

Hom.:

277

Cov.:

AF XY:

0.0373

AC XY:

2781

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00914

Gnomad4 AMR

AF:

0.0894

Gnomad4 ASJ

AF:

0.00979

Gnomad4 EAS

AF:

0.261

Gnomad4 SAS

AF:

0.0215

Gnomad4 FIN

AF:

0.0317

Gnomad4 NFE

AF:

0.0246

Gnomad4 OTH

AF:

0.0284

Alfa

AF:

0.0239

Hom.:

Bravo

AF:

0.0395

Asia WGS

AF:

0.120

AC:

415

AN:

3478

EpiCase

AF:

0.0213

EpiControl

AF:

0.0219

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

JMJD1C-related disorder

Benign:1

Mar 21, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Early myoclonic encephalopathy

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over