rs7804356

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003930.5(SKAP2):​c.199+2091A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,030 control chromosomes in the GnomAD database, including 3,585 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 0.21 ( 3585 hom., cov: 31)

Consequence

SKAP2
NM_003930.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.101
Variant links:
Genes affected
SKAP2 (HGNC:15687): (src kinase associated phosphoprotein 2) The protein encoded by this gene shares homology with Src kinase-associated phosphoprotein 1, and is a substrate of Src family kinases. It is an adaptor protein that is thought to play an essential role in the Src signaling pathway, and in regulating proper activation of the immune system. This protein contains an amino terminal coiled-coil domain for self-dimerization, a plecskstrin homology (PH) domain required for interactions with lipids at the membrane, and a Src homology (SH3) domain at the carboxy terminus. Some reports indicate that this protein inhibits actin polymerization through interactions with actin assembly factors, and might negatively regulate the invasiveness of tumors by modulating actin assembly. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SKAP2NM_003930.5 linkuse as main transcriptc.199+2091A>G intron_variant ENST00000345317.7
LOC124901606XR_007060265.1 linkuse as main transcriptn.201-5418T>C intron_variant, non_coding_transcript_variant
SKAP2NM_001303468.2 linkuse as main transcriptc.-318+2091A>G intron_variant
SKAP2XM_017012771.3 linkuse as main transcriptc.199+2091A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SKAP2ENST00000345317.7 linkuse as main transcriptc.199+2091A>G intron_variant 1 NM_003930.5 P1

Frequencies

GnomAD3 genomes
AF:
0.214
AC:
32559
AN:
151912
Hom.:
3587
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.188
Gnomad AMI
AF:
0.344
Gnomad AMR
AF:
0.225
Gnomad ASJ
AF:
0.268
Gnomad EAS
AF:
0.0960
Gnomad SAS
AF:
0.221
Gnomad FIN
AF:
0.190
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.236
Gnomad OTH
AF:
0.212
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.214
AC:
32568
AN:
152030
Hom.:
3585
Cov.:
31
AF XY:
0.212
AC XY:
15778
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.188
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.268
Gnomad4 EAS
AF:
0.0963
Gnomad4 SAS
AF:
0.221
Gnomad4 FIN
AF:
0.190
Gnomad4 NFE
AF:
0.236
Gnomad4 OTH
AF:
0.209
Alfa
AF:
0.231
Hom.:
6345
Bravo
AF:
0.216
Asia WGS
AF:
0.156
AC:
544
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
5.8
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: rs7804356; hg19: chr7-26891665; API