rs6968355

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_182692.3(SRPK2):​c.*35A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,607,548 control chromosomes in the GnomAD database, including 30,542 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 0.14 ( 2053 hom., cov: 33)
Exomes 𝑓: 0.19 ( 28489 hom. )

Consequence

SRPK2
NM_182692.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.756
Variant links:
Genes affected
SRPK2 (HGNC:11306): (SRSF protein kinase 2) Enables ATP binding activity; magnesium ion binding activity; and protein serine/threonine kinase activity. Involved in several processes, including nucleic acid metabolic process; peptidyl-serine phosphorylation; and regulation of viral genome replication. Located in chromatin; cytosol; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRPK2NM_182692.3 linkuse as main transcriptc.*35A>G 3_prime_UTR_variant 16/16 ENST00000393651.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRPK2ENST00000393651.8 linkuse as main transcriptc.*35A>G 3_prime_UTR_variant 16/162 NM_182692.3 P2P78362-2

Frequencies

GnomAD3 genomes
AF:
0.142
AC:
21648
AN:
152154
Hom.:
2054
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0361
Gnomad AMI
AF:
0.121
Gnomad AMR
AF:
0.211
Gnomad ASJ
AF:
0.138
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.186
Gnomad FIN
AF:
0.216
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.189
Gnomad OTH
AF:
0.141
GnomAD3 exomes
AF:
0.181
AC:
45067
AN:
248928
Hom.:
5085
AF XY:
0.181
AC XY:
24379
AN XY:
134686
show subpopulations
Gnomad AFR exome
AF:
0.0297
Gnomad AMR exome
AF:
0.322
Gnomad ASJ exome
AF:
0.125
Gnomad EAS exome
AF:
0.000987
Gnomad SAS exome
AF:
0.196
Gnomad FIN exome
AF:
0.213
Gnomad NFE exome
AF:
0.184
Gnomad OTH exome
AF:
0.175
GnomAD4 exome
AF:
0.190
AC:
276711
AN:
1455276
Hom.:
28489
Cov.:
29
AF XY:
0.191
AC XY:
138265
AN XY:
724176
show subpopulations
Gnomad4 AFR exome
AF:
0.0278
Gnomad4 AMR exome
AF:
0.307
Gnomad4 ASJ exome
AF:
0.130
Gnomad4 EAS exome
AF:
0.00103
Gnomad4 SAS exome
AF:
0.200
Gnomad4 FIN exome
AF:
0.210
Gnomad4 NFE exome
AF:
0.198
Gnomad4 OTH exome
AF:
0.174
GnomAD4 genome
AF:
0.142
AC:
21644
AN:
152272
Hom.:
2053
Cov.:
33
AF XY:
0.144
AC XY:
10701
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.0360
Gnomad4 AMR
AF:
0.211
Gnomad4 ASJ
AF:
0.138
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.186
Gnomad4 FIN
AF:
0.216
Gnomad4 NFE
AF:
0.189
Gnomad4 OTH
AF:
0.139
Alfa
AF:
0.183
Hom.:
1355
Bravo
AF:
0.138
Asia WGS
AF:
0.0770
AC:
267
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.44
CADD
Benign
10
DANN
Benign
0.77

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: rs6968355; hg19: chr7-104758250; COSMIC: COSV57581065; COSMIC: COSV57581065; API