rs7896783

chr10-63402393-G-Achr10-63402393-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032776.3(JMJD1C):c.169-21911C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,962 control chromosomes in the GnomAD database, including 14,230 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 0.42 (14230 hom., cov: 32)
• Consequence: JMJD1C NM_032776.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JMJD1C	NM_032776.3	c.169-21911C>T		intron_variant		ENST00000399262.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JMJD1C	ENST00000399262.7	c.169-21911C>T		intron_variant		5	NM_032776.3
JMJD1C	ENST00000633035.1	n.114-21911C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64029 AN: 151844 Hom.: 14245 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.421 AC: 64002 AN: 151962 Hom.: 14230 Cov.: 32 AF XY: 0.421 AC XY: 31257 AN XY: 74268

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.425

Alfa AF: 0.465 Hom.: 26524

Bravo AF: 0.398

Asia WGS AF: 0.432 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.5
Dann	Benign	0.72

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: rs7896783; hg19: chr10-65162153;