Genetic Variant JMJD6:c.1209-82C>T (chr17-76716804-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.82

Publications

16 publications found

Variant links:

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]

JMJD6 links:

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ACMG classification

Classification was made for transcript

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 link	c.1209-82C>T		intron_variant	Intron 6 of 6		NP_001074930.1	Q6NYC1-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JMJD6	ENST00000445478.6 link	c.1209-82C>T		intron_variant	Intron 6 of 6	1		ENSP00000394085.2		Q6NYC1-3
JMJD6	ENST00000617192.4 link	c.*217-82C>T		intron_variant	Intron 7 of 7	5		ENSP00000483941.1		B2WTI4

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20702

AN:

152054

Hom.:

1688

Cov.:

show subpopulations

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

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

5917

11834

17750

23667

29584

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3528

7056

10584

14112

17640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.136

AC:

20724

AN:

152172

Hom.:

1692

Cov.:

AF XY:

0.135

AC XY:

10073

AN XY:

74406

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0943

AC:

6415

AN:

68000

Other (OTH)

AF:

0.129

AC:

273

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

894

1788

2683

3577

4471

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

226

452

678

904

1130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.87

PhyloP100

1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over