chr7-26725466-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003930.5(SKAP2):c.758G>C(p.Ser253Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00303 in 1,611,884 control chromosomes in the GnomAD database, including 118 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003930.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SKAP2 | NM_003930.5 | c.758G>C | p.Ser253Thr | missense_variant | 9/13 | ENST00000345317.7 | |
SKAP2 | NM_001303468.2 | c.242G>C | p.Ser81Thr | missense_variant | 9/13 | ||
SKAP2 | XM_017012771.3 | c.758G>C | p.Ser253Thr | missense_variant | 9/13 | ||
SKAP2 | XM_047421010.1 | c.242G>C | p.Ser81Thr | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKAP2 | ENST00000345317.7 | c.758G>C | p.Ser253Thr | missense_variant | 9/13 | 1 | NM_003930.5 | P1 | |
SKAP2 | ENST00000489977.5 | n.585G>C | non_coding_transcript_exon_variant | 6/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0159 AC: 2418AN: 151944Hom.: 61 Cov.: 32
GnomAD3 exomes AF: 0.00430 AC: 1074AN: 249626Hom.: 25 AF XY: 0.00310 AC XY: 419AN XY: 135002
GnomAD4 exome AF: 0.00168 AC: 2459AN: 1459822Hom.: 56 Cov.: 31 AF XY: 0.00142 AC XY: 1029AN XY: 726268
GnomAD4 genome ? AF: 0.0159 AC: 2420AN: 152062Hom.: 62 Cov.: 32 AF XY: 0.0155 AC XY: 1150AN XY: 74346
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at