X-102715045-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001004051.4(GPRASP2):c.176C>T(p.Ala59Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000504 in 1,211,156 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 27 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004051.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPRASP2 | NM_001004051.4 | c.176C>T | p.Ala59Val | missense_variant | 5/5 | ENST00000483720.7 | |
ARMCX5-GPRASP2 | NR_146584.3 | n.795+779C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPRASP2 | ENST00000483720.7 | c.176C>T | p.Ala59Val | missense_variant | 5/5 | 2 | NM_001004051.4 | P1 | |
ARMCX5-GPRASP2 | ENST00000652409.1 | c.-756+779C>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000443 AC: 5AN: 112950Hom.: 0 Cov.: 24 AF XY: 0.0000568 AC XY: 2AN XY: 35188
GnomAD3 exomes AF: 0.0000982 AC: 18AN: 183362Hom.: 0 AF XY: 0.000103 AC XY: 7AN XY: 67824
GnomAD4 exome AF: 0.0000510 AC: 56AN: 1098206Hom.: 0 Cov.: 31 AF XY: 0.0000688 AC XY: 25AN XY: 363574
GnomAD4 genome AF: 0.0000443 AC: 5AN: 112950Hom.: 0 Cov.: 24 AF XY: 0.0000568 AC XY: 2AN XY: 35188
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 13, 2024 | The c.176C>T (p.A59V) alteration is located in exon 5 (coding exon 1) of the GPRASP2 gene. This alteration results from a C to T substitution at nucleotide position 176, causing the alanine (A) at amino acid position 59 to be replaced by a valine (V). 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