NM_178860.5:c.1240+10dupC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_178860.5(SEZ6):​c.1240+10dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 1,604,148 control chromosomes in the GnomAD database, including 228,868 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 31201 hom., cov: 0)
Exomes 𝑓: 0.52 ( 197667 hom. )

Consequence

SEZ6
NM_178860.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.265

Publications

6 publications found
Variant links:
Genes affected
SEZ6 (HGNC:15955): (seizure related 6 homolog) The protein encoded by this gene is thought to contain five cysteine-rich motifs that are similar to sushi domains, as well as two domains similar to the amino terminal half of the CUB (for complement C1r/C1s, Uegf, Bmp1) domain. Mutations in this gene have been associated with febrile seizures. [provided by RefSeq, Jul 2016]
PIPOX (HGNC:17804): (pipecolic acid and sarcosine oxidase) Enables L-pipecolate oxidase activity and sarcosine oxidase activity. Involved in L-lysine catabolic process to acetyl-CoA via L-pipecolate. Located in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SEZ6NM_178860.5 linkc.1240+10dupC intron_variant Intron 5 of 16 ENST00000317338.17 NP_849191.3 Q53EL9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SEZ6ENST00000317338.17 linkc.1240+10_1240+11insC intron_variant Intron 5 of 16 1 NM_178860.5 ENSP00000312942.11 Q53EL9-1

Frequencies

GnomAD3 genomes
AF:
0.614
AC:
93263
AN:
151978
Hom.:
31150
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.900
Gnomad AMI
AF:
0.533
Gnomad AMR
AF:
0.520
Gnomad ASJ
AF:
0.514
Gnomad EAS
AF:
0.322
Gnomad SAS
AF:
0.528
Gnomad FIN
AF:
0.543
Gnomad MID
AF:
0.573
Gnomad NFE
AF:
0.507
Gnomad OTH
AF:
0.591
GnomAD2 exomes
AF:
0.514
AC:
119382
AN:
232150
AF XY:
0.512
show subpopulations
Gnomad AFR exome
AF:
0.909
Gnomad AMR exome
AF:
0.440
Gnomad ASJ exome
AF:
0.515
Gnomad EAS exome
AF:
0.327
Gnomad FIN exome
AF:
0.542
Gnomad NFE exome
AF:
0.503
Gnomad OTH exome
AF:
0.519
GnomAD4 exome
AF:
0.516
AC:
749236
AN:
1452052
Hom.:
197667
Cov.:
41
AF XY:
0.515
AC XY:
371361
AN XY:
721280
show subpopulations
African (AFR)
AF:
0.920
AC:
30670
AN:
33330
American (AMR)
AF:
0.452
AC:
19595
AN:
43366
Ashkenazi Jewish (ASJ)
AF:
0.517
AC:
13392
AN:
25900
East Asian (EAS)
AF:
0.334
AC:
13185
AN:
39434
South Asian (SAS)
AF:
0.532
AC:
44866
AN:
84294
European-Finnish (FIN)
AF:
0.537
AC:
28314
AN:
52760
Middle Eastern (MID)
AF:
0.569
AC:
3247
AN:
5704
European-Non Finnish (NFE)
AF:
0.510
AC:
564250
AN:
1107268
Other (OTH)
AF:
0.529
AC:
31717
AN:
59996
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.486
Heterozygous variant carriers
0
19007
38014
57020
76027
95034
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
16416
32832
49248
65664
82080
<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:
0.614
AC:
93361
AN:
152096
Hom.:
31201
Cov.:
0
AF XY:
0.611
AC XY:
45425
AN XY:
74360
show subpopulations
African (AFR)
AF:
0.900
AC:
37367
AN:
41516
American (AMR)
AF:
0.520
AC:
7948
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.514
AC:
1783
AN:
3470
East Asian (EAS)
AF:
0.322
AC:
1662
AN:
5166
South Asian (SAS)
AF:
0.526
AC:
2534
AN:
4820
European-Finnish (FIN)
AF:
0.543
AC:
5743
AN:
10568
Middle Eastern (MID)
AF:
0.571
AC:
168
AN:
294
European-Non Finnish (NFE)
AF:
0.507
AC:
34436
AN:
67968
Other (OTH)
AF:
0.585
AC:
1235
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1610
3219
4829
6438
8048
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
740
1480
2220
2960
3700
<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:
0.549
Hom.:
5350
Bravo
AF:
0.623
Asia WGS
AF:
0.452
AC:
1574
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.27
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs11450637; hg19: chr17-27290969; API