GeneBe

rs2423279

Variant names:

Variant summary

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

The variant allele was found at a frequency of 0.292 in 294,204 control chromosomes in the GnomAD database, including 13,942 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 0.29 ( 6895 hom., cov: 33)
Exomes 𝑓: 0.29 ( 7047 hom. )

Consequence

SRSF10P2
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0250

Publications

68 publications found
Variant links:
Genes affected

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=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SRSF10P2 n.7831703T>C intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SRSF10P2ENST00000400616.2 linkn.*95A>G downstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.293
AC:
44535
AN:
152020
Hom.:
6874
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.353
Gnomad AMI
AF:
0.276
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.338
Gnomad EAS
AF:
0.325
Gnomad SAS
AF:
0.487
Gnomad FIN
AF:
0.205
Gnomad MID
AF:
0.316
Gnomad NFE
AF:
0.248
Gnomad OTH
AF:
0.309
GnomAD4 exome
AF:
0.290
AC:
41269
AN:
142066
Hom.:
7047
AF XY:
0.303
AC XY:
23257
AN XY:
76826
show subpopulations
African (AFR)
AF:
0.350
AC:
1732
AN:
4946
American (AMR)
AF:
0.336
AC:
3156
AN:
9398
Ashkenazi Jewish (ASJ)
AF:
0.314
AC:
1329
AN:
4226
East Asian (EAS)
AF:
0.293
AC:
2891
AN:
9860
South Asian (SAS)
AF:
0.474
AC:
8927
AN:
18822
European-Finnish (FIN)
AF:
0.213
AC:
1688
AN:
7910
Middle Eastern (MID)
AF:
0.335
AC:
181
AN:
540
European-Non Finnish (NFE)
AF:
0.244
AC:
19224
AN:
78818
Other (OTH)
AF:
0.284
AC:
2141
AN:
7546
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.515
Heterozygous variant carriers
0
1338
2676
4014
5352
6690
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
272
544
816
1088
1360
<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:
0.293
AC:
44605
AN:
152138
Hom.:
6895
Cov.:
33
AF XY:
0.293
AC XY:
21759
AN XY:
74386
show subpopulations
African (AFR)
AF:
0.353
AC:
14663
AN:
41490
American (AMR)
AF:
0.306
AC:
4681
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.338
AC:
1172
AN:
3468
East Asian (EAS)
AF:
0.325
AC:
1680
AN:
5168
South Asian (SAS)
AF:
0.486
AC:
2346
AN:
4826
European-Finnish (FIN)
AF:
0.205
AC:
2175
AN:
10606
Middle Eastern (MID)
AF:
0.310
AC:
91
AN:
294
European-Non Finnish (NFE)
AF:
0.248
AC:
16878
AN:
67974
Other (OTH)
AF:
0.316
AC:
668
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1621
3242
4862
6483
8104
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
462
924
1386
1848
2310
<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:
0.268
Hom.:
13490
Bravo
AF:
0.302
Asia WGS
AF:
0.446
AC:
1548
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
9.7
DANN
Benign
0.42
PhyloP100
-0.025

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2423279; hg19: chr20-7812350; COSMIC: COSV68763360; API