rs10761779

chr10-63515167-A-Gchr10-63515167-A-T

Variant summary

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

The NM_001318154.2(JMJD1C):c.-379+6571T>C 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 151,852 control chromosomes in the GnomAD database, including 14,174 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 (14174 hom., cov: 31)
• Consequence: JMJD1C NM_001318154.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JMJD1C	NM_001318154.2	c.-379+6571T>C		intron_variant
JMJD1C	NM_001322258.2	c.-384+6571T>C		intron_variant
JMJD1C	XM_011539508.3	c.-445+6571T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JMJD1C	ENST00000633035.1	n.113+6571T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63921 AN: 151734 Hom.: 14188 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.488

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: 63896 AN: 151852 Hom.: 14174 Cov.: 31 AF XY: 0.421 AC XY: 31214 AN XY: 74198

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.426

Alfa AF: 0.467 Hom.: 30441

Bravo AF: 0.398

Asia WGS AF: 0.434 AC: 1511 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	2.4
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10761779; hg19: chr10-65274927;