1-17373219-G-T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2

The NM_207421.4(PADI6):​c.280G>T​(p.Val94Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,613,898 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V94M) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 2 hom. )

Consequence

PADI6
NM_207421.4 missense

Scores

10

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: -2.42
Variant links:
Genes affected
PADI6 (HGNC:20449): (peptidyl arginine deiminase 6) This gene encodes a member of the peptidyl arginine deiminase family of enzymes, which catalyze the post-translational deimination of proteins by converting arginine residues into citrullines in the presence of calcium ions. The family members have distinct substrate specificities and tissue-specific expression patterns. This protein may play a role in cytoskeletal reorganization in the egg and in early embryo development. [provided by RefSeq, Sep 2012]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.008853823).
BS1
Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00101 (154/152272) while in subpopulation NFE AF = 0.00191 (130/68024). AF 95% confidence interval is 0.00164. There are 0 homozygotes in GnomAd4. There are 66 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PADI6NM_207421.4 linkc.280G>T p.Val94Leu missense_variant Exon 2 of 16 ENST00000619609.1 NP_997304.3 Q6TGC4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PADI6ENST00000619609.1 linkc.280G>T p.Val94Leu missense_variant Exon 2 of 16 1 NM_207421.4 ENSP00000483125.1 Q6TGC4

Frequencies

GnomAD3 genomes
AF:
0.00101
AC:
154
AN:
152154
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000265
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000590
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000283
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00191
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.000791
AC:
197
AN:
248974
AF XY:
0.000770
show subpopulations
Gnomad AFR exome
AF:
0.000258
Gnomad AMR exome
AF:
0.000174
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000325
Gnomad NFE exome
AF:
0.00153
Gnomad OTH exome
AF:
0.00116
GnomAD4 exome
AF:
0.00136
AC:
1991
AN:
1461626
Hom.:
2
Cov.:
31
AF XY:
0.00132
AC XY:
959
AN XY:
727110
show subpopulations
Gnomad4 AFR exome
AF:
0.000269
AC:
9
AN:
33480
Gnomad4 AMR exome
AF:
0.000224
AC:
10
AN:
44718
Gnomad4 ASJ exome
AF:
0.0000383
AC:
1
AN:
26130
Gnomad4 EAS exome
AF:
0.00
AC:
0
AN:
39696
Gnomad4 SAS exome
AF:
0.00
AC:
0
AN:
86254
Gnomad4 FIN exome
AF:
0.000449
AC:
24
AN:
53396
Gnomad4 NFE exome
AF:
0.00171
AC:
1902
AN:
1111820
Gnomad4 Remaining exome
AF:
0.000745
AC:
45
AN:
60370
Heterozygous variant carriers
0
114
227
341
454
568
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
74
148
222
296
370
<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:
0.00101
AC:
154
AN:
152272
Hom.:
0
Cov.:
32
AF XY:
0.000887
AC XY:
66
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.000265
AC:
0.000264627
AN:
0.000264627
Gnomad4 AMR
AF:
0.000589
AC:
0.000588774
AN:
0.000588774
Gnomad4 ASJ
AF:
0.00
AC:
0
AN:
0
Gnomad4 EAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 SAS
AF:
0.00
AC:
0
AN:
0
Gnomad4 FIN
AF:
0.000283
AC:
0.000282592
AN:
0.000282592
Gnomad4 NFE
AF:
0.00191
AC:
0.00191109
AN:
0.00191109
Gnomad4 OTH
AF:
0.00
AC:
0
AN:
0
Heterozygous variant carriers
0
7
13
20
26
33
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Variant carriers
0
4
8
12
16
20
<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:
0.00111
Hom.:
0
Bravo
AF:
0.00101
TwinsUK
AF:
0.00135
AC:
5
ALSPAC
AF:
0.00156
AC:
6
ESP6500AA
AF:
0.000232
AC:
1
ESP6500EA
AF:
0.00188
AC:
16
ExAC
AF:
0.000751
AC:
91

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Sep 16, 2021
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The c.280G>T (p.V94L) alteration is located in exon 2 (coding exon 2) of the PADI6 gene. This alteration results from a G to T substitution at nucleotide position 280, causing the valine (V) at amino acid position 94 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

not provided Uncertain:1
Feb 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.51
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
0.0020
DANN
Benign
0.65
DEOGEN2
Benign
0.0052
T
FATHMM_MKL
Benign
0.040
N
MetaRNN
Benign
0.0089
T
MutationAssessor
Benign
0.76
N
PrimateAI
Benign
0.27
T
Sift4G
Benign
0.77
T
Vest4
0.070
MVP
0.061
GERP RS
-6.5
Varity_R
0.030
gMVP
0.12

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs200488264; hg19: chr1-17699714; COSMIC: COSV61884109; API