chr11-64197520-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006819.3(STIP1):c.827A>G(p.Asn276Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,614,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N276D) has been classified as Uncertain significance.
Frequency
Consequence
NM_006819.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STIP1 | NM_006819.3 | c.827A>G | p.Asn276Ser | missense_variant | 7/14 | ENST00000305218.9 | |
STIP1 | NM_001282652.2 | c.968A>G | p.Asn323Ser | missense_variant | 7/14 | ||
STIP1 | NM_001282653.2 | c.755A>G | p.Asn252Ser | missense_variant | 7/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STIP1 | ENST00000305218.9 | c.827A>G | p.Asn276Ser | missense_variant | 7/14 | 1 | NM_006819.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251456Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135906
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727244
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.827A>G (p.N276S) alteration is located in exon 7 (coding exon 7) of the STIP1 gene. This alteration results from a A to G substitution at nucleotide position 827, causing the asparagine (N) at amino acid position 276 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at