chrX-102655460-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001184727.2(GPRASP1):āc.1547C>Gā(p.Thr516Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000496 in 1,209,152 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 180 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001184727.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPRASP1 | NM_001184727.2 | c.1547C>G | p.Thr516Ser | missense_variant | 6/6 | ENST00000537097.2 | |
ARMCX5-GPRASP2 | NR_146584.3 | n.649+49807C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPRASP1 | ENST00000537097.2 | c.1547C>G | p.Thr516Ser | missense_variant | 6/6 | 2 | NM_001184727.2 | P1 | |
ENST00000602441.1 | n.57+4196G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000234 AC: 26AN: 111170Hom.: 0 Cov.: 23 AF XY: 0.000209 AC XY: 7AN XY: 33418
GnomAD3 exomes AF: 0.000234 AC: 43AN: 183521Hom.: 0 AF XY: 0.000221 AC XY: 15AN XY: 67951
GnomAD4 exome AF: 0.000523 AC: 574AN: 1097982Hom.: 0 Cov.: 32 AF XY: 0.000476 AC XY: 173AN XY: 363336
GnomAD4 genome AF: 0.000234 AC: 26AN: 111170Hom.: 0 Cov.: 23 AF XY: 0.000209 AC XY: 7AN XY: 33418
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | The c.1547C>G (p.T516S) alteration is located in exon 6 (coding exon 1) of the GPRASP1 gene. This alteration results from a C to G substitution at nucleotide position 1547, causing the threonine (T) at amino acid position 516 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | GPRASP1: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at