rs1014390

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001081461.2(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
NM_001081461.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.82
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]

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ACMG classification

Classification made for transcript

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 rank MANE Protein UniProt
JMJD6NM_001081461.2 linkc.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
JMJD6ENST00000445478.6 linkc.1209-82C>T intron_variant Intron 6 of 6 1 ENSP00000394085.2 Q6NYC1-3
JMJD6ENST00000617192.4 linkc.*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.:
32
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
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
show subpopulations
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1014390; hg19: chr17-74712886; API