chr7-29922908-C-T

Variant summary

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

The NM_014766.5(SCRN1):​c.*1049G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0591 in 152,244 control chromosomes in the GnomAD database, including 423 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 0.059 ( 423 hom., cov: 33)
Exomes 𝑓: 0.13 ( 0 hom. )

Consequence

SCRN1
NM_014766.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0870

Publications

11 publications found
Variant links:
Genes affected
SCRN1 (HGNC:22192): (secernin 1) This gene likely encodes a member of the secernin family of proteins. A similar protein in rat functions in regulation of exocytosis in mast cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]

Genome browser will be placed here

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 (AMR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCRN1NM_014766.5 linkc.*1049G>A 3_prime_UTR_variant Exon 8 of 8 ENST00000242059.10 NP_055581.3 Q12765-1A0A090N7T9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCRN1ENST00000242059.10 linkc.*1049G>A 3_prime_UTR_variant Exon 8 of 8 1 NM_014766.5 ENSP00000242059.5 Q12765-1
SCRN1ENST00000426154.5 linkc.*1049G>A 3_prime_UTR_variant Exon 8 of 8 5 ENSP00000409068.1 Q12765-1

Frequencies

GnomAD3 genomes
AF:
0.0592
AC:
9007
AN:
152118
Hom.:
424
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0165
Gnomad AMI
AF:
0.0165
Gnomad AMR
AF:
0.144
Gnomad ASJ
AF:
0.0153
Gnomad EAS
AF:
0.00346
Gnomad SAS
AF:
0.0431
Gnomad FIN
AF:
0.0454
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0769
Gnomad OTH
AF:
0.0526
GnomAD4 exome
AF:
0.125
AC:
1
AN:
8
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
4
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.167
AC:
1
AN:
6
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.0591
AC:
9001
AN:
152236
Hom.:
423
Cov.:
33
AF XY:
0.0586
AC XY:
4359
AN XY:
74424
show subpopulations
African (AFR)
AF:
0.0164
AC:
683
AN:
41548
American (AMR)
AF:
0.144
AC:
2197
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.0153
AC:
53
AN:
3472
East Asian (EAS)
AF:
0.00347
AC:
18
AN:
5188
South Asian (SAS)
AF:
0.0428
AC:
206
AN:
4818
European-Finnish (FIN)
AF:
0.0454
AC:
481
AN:
10586
Middle Eastern (MID)
AF:
0.0374
AC:
11
AN:
294
European-Non Finnish (NFE)
AF:
0.0769
AC:
5227
AN:
68008
Other (OTH)
AF:
0.0520
AC:
110
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
433
866
1300
1733
2166
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
104
208
312
416
520
<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:
0.0778
Hom.:
281
Bravo
AF:
0.0649
Asia WGS
AF:
0.0240
AC:
83
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
0.75
PhyloP100
-0.087
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs17158483; hg19: chr7-29962524; API