chr1-110034674-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033088.4(STRIP1):c.37G>T(p.Val13Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000918 in 1,524,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033088.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STRIP1 | NM_033088.4 | c.37G>T | p.Val13Leu | missense_variant | 1/21 | ENST00000369795.8 | |
LOC105378895 | XR_947693.3 | n.31+735C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRIP1 | ENST00000369795.8 | c.37G>T | p.Val13Leu | missense_variant | 1/21 | 1 | NM_033088.4 | P1 | |
STRIP1 | ENST00000485775.5 | c.37G>T | p.Val13Leu | missense_variant, NMD_transcript_variant | 1/22 | 1 | |||
STRIP1 | ENST00000369796.5 | c.-106+3034G>T | intron_variant | 2 | |||||
STRIP1 | ENST00000489059.1 | n.49G>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000875 AC: 12AN: 1372200Hom.: 0 Cov.: 31 AF XY: 0.00000295 AC XY: 2AN XY: 677006
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2022 | The c.37G>T (p.V13L) alteration is located in exon 1 (coding exon 1) of the STRIP1 gene. This alteration results from a G to T substitution at nucleotide position 37, causing the valine (V) at amino acid position 13 to be replaced by a leucine (L). 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