rs1014390

Variant names:

• chr17-76716804-G-A
• rs1014390
• ENST00000445478.6:c.1209-82C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-76716804-G-A
• chr17-76716804-G-C
• chr17-76716804-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
JMJD6	NM_001081461.2	c.1209-82C>T		intron_variant	Intron 6 of 6		NP_001074930.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JMJD6	ENST00000445478.6	c.1209-82C>T		intron_variant	Intron 6 of 6	1		ENSP00000394085.2
JMJD6	ENST00000617192.4	c.*217-82C>T		intron_variant	Intron 7 of 7	5		ENSP00000483941.1

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

African (AFR) AF: 0.227 AC: 6764 AN: 29802

American (AMR) AF: 0.125 AC: 5409 AN: 43208

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 2346 AN: 24516

East Asian (EAS) AF: 0.180 AC: 6969 AN: 38618

South Asian (SAS) AF: 0.0786 AC: 6404 AN: 81426

European-Finnish (FIN) AF: 0.137 AC: 7230 AN: 52954

Middle Eastern (MID) AF: 0.105 AC: 560 AN: 5310

European-Non Finnish (NFE) AF: 0.102 AC: 95483 AN: 931812

Other (OTH) AF: 0.118 AC: 6332 AN: 53558

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

African (AFR) AF: 0.221 AC: 9166 AN: 41474

American (AMR) AF: 0.122 AC: 1870 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.171 AC: 885 AN: 5180

South Asian (SAS) AF: 0.0751 AC: 363 AN: 4832

European-Finnish (FIN) AF: 0.131 AC: 1388 AN: 10606

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0943 AC: 6415 AN: 68000

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.108 Hom.: 3228

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
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1014390; hg19: chr17-74712886;