chr17-48313716-C-T

Variant summary

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

The NM_003726.4(SKAP1):​c.280+32189G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,998 control chromosomes in the GnomAD database, including 9,161 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 0.33 ( 9161 hom., cov: 32)

Consequence

SKAP1
NM_003726.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0980

Publications

8 publications found
Variant links:
Genes affected
SKAP1 (HGNC:15605): (src kinase associated phosphoprotein 1) This gene encodes a T cell adaptor protein, a class of intracellular molecules with modular domains capable of recruiting additional proteins but that exhibit no intrinsic enzymatic activity. The encoded protein contains a unique N-terminal region followed by a PH domain and C-terminal SH3 domain. Along with the adhesion and degranulation-promoting adaptor protein, the encoded protein plays a critical role in inside-out signaling by coupling T-cell antigen receptor stimulation to the activation of integrins. [provided by RefSeq, Jul 2008]

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=-0.54).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SKAP1NM_003726.4 linkc.280+32189G>A intron_variant Intron 4 of 12 ENST00000336915.11 NP_003717.3 Q86WV1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SKAP1ENST00000336915.11 linkc.280+32189G>A intron_variant Intron 4 of 12 1 NM_003726.4 ENSP00000338171.6 Q86WV1-1

Frequencies

GnomAD3 genomes
AF:
0.334
AC:
50694
AN:
151880
Hom.:
9152
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.469
Gnomad AMI
AF:
0.308
Gnomad AMR
AF:
0.390
Gnomad ASJ
AF:
0.298
Gnomad EAS
AF:
0.178
Gnomad SAS
AF:
0.186
Gnomad FIN
AF:
0.268
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.274
Gnomad OTH
AF:
0.319
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.334
AC:
50729
AN:
151998
Hom.:
9161
Cov.:
32
AF XY:
0.331
AC XY:
24582
AN XY:
74316
show subpopulations
African (AFR)
AF:
0.469
AC:
19437
AN:
41436
American (AMR)
AF:
0.391
AC:
5968
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.298
AC:
1035
AN:
3468
East Asian (EAS)
AF:
0.177
AC:
916
AN:
5172
South Asian (SAS)
AF:
0.186
AC:
897
AN:
4824
European-Finnish (FIN)
AF:
0.268
AC:
2826
AN:
10548
Middle Eastern (MID)
AF:
0.262
AC:
77
AN:
294
European-Non Finnish (NFE)
AF:
0.274
AC:
18630
AN:
67970
Other (OTH)
AF:
0.314
AC:
663
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1682
3364
5045
6727
8409
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
466
932
1398
1864
2330
<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:
0.294
Hom.:
3501
Bravo
AF:
0.354
Asia WGS
AF:
0.221
AC:
771
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
14
DANN
Benign
0.65
PhyloP100
0.098
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: rs12452212; hg19: chr17-46391078; API