rs1014390

chr17-76716804-G-Achr17-76716804-G-Cchr17-76716804-G-T

Variant summary

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

The ENST00000445478.6(JMJD6):c.1209-82C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,413,376 control chromosomes in the GnomAD database, including 9,295 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 0.14 (1692 hom., cov: 32)
  • Exomes 𝑓: 0.11 (7603 hom.)
• Consequence: JMJD6 ENST00000445478.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

Genes affected

JMJD6 (HGNC:19355): (jumonji domain containing 6, arginine demethylase and lysine hydroxylase) This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins are predicted to function as protein hydroxylases or histone demethylases. This protein was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that it does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JMJD6	NM_001081461.2	c.1209-82C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JMJD6	ENST00000445478.6	c.1209-82C>T		intron_variant		1
JMJD6	ENST00000617192.4	c.*217-82C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20702 AN: 152054 Hom.: 1688 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0751

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.109 AC: 137497 AN: 1261204 Hom.: 7603 AF XY: 0.107 AC XY: 68002 AN XY: 634730

Gnomad4 AFR exome AF: 0.227

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.0957

Gnomad4 EAS exome AF: 0.180

Gnomad4 SAS exome AF: 0.0786

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.118

GnomAD4 genome AF: 0.136 AC: 20724 AN: 152172 Hom.: 1692 Cov.: 32 AF XY: 0.135 AC XY: 10073 AN XY: 74406

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0751

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0951 Hom.: 1032

Bravo AF: 0.141

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	11
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1014390; hg19: chr17-74712886;