chr1-31425689-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178865.5(SERINC2):c.473-87C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 1,470,186 control chromosomes in the GnomAD database, including 211,129 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 0.44 ( 16945 hom., cov: 33)
Exomes 𝑓: 0.53 ( 194184 hom. )
Consequence
SERINC2
NM_178865.5 intron
NM_178865.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.394
Publications
11 publications found
Genes affected
SERINC2 (HGNC:23231): (serine incorporator 2) Predicted to be involved in several processes, including phosphatidylserine metabolic process; positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity; and positive regulation of serine C-palmitoyltransferase activity. Located in extracellular exosome. [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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.441 AC: 66941AN: 151918Hom.: 16944 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
66941
AN:
151918
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.533 AC: 702842AN: 1318150Hom.: 194184 AF XY: 0.530 AC XY: 346747AN XY: 654458 show subpopulations
GnomAD4 exome
AF:
AC:
702842
AN:
1318150
Hom.:
AF XY:
AC XY:
346747
AN XY:
654458
show subpopulations
African (AFR)
AF:
AC:
6028
AN:
30864
American (AMR)
AF:
AC:
18626
AN:
40300
Ashkenazi Jewish (ASJ)
AF:
AC:
12455
AN:
22182
East Asian (EAS)
AF:
AC:
7107
AN:
38832
South Asian (SAS)
AF:
AC:
27300
AN:
74998
European-Finnish (FIN)
AF:
AC:
25274
AN:
46982
Middle Eastern (MID)
AF:
AC:
1912
AN:
3750
European-Non Finnish (NFE)
AF:
AC:
576235
AN:
1005192
Other (OTH)
AF:
AC:
27905
AN:
55050
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
15843
31687
47530
63374
79217
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
15420
30840
46260
61680
77100
<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: 0.440 AC: 66942AN: 152036Hom.: 16945 Cov.: 33 AF XY: 0.437 AC XY: 32471AN XY: 74330 show subpopulations
GnomAD4 genome
AF:
AC:
66942
AN:
152036
Hom.:
Cov.:
33
AF XY:
AC XY:
32471
AN XY:
74330
show subpopulations
African (AFR)
AF:
AC:
8719
AN:
41454
American (AMR)
AF:
AC:
7435
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
1929
AN:
3464
East Asian (EAS)
AF:
AC:
1052
AN:
5164
South Asian (SAS)
AF:
AC:
1678
AN:
4832
European-Finnish (FIN)
AF:
AC:
5601
AN:
10584
Middle Eastern (MID)
AF:
AC:
151
AN:
292
European-Non Finnish (NFE)
AF:
AC:
38994
AN:
67948
Other (OTH)
AF:
AC:
980
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1788
3575
5363
7150
8938
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
602
1204
1806
2408
3010
<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:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.