chrX-102655530-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001184727.2(GPRASP1):c.1617G>T(p.Glu539Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 1,209,510 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 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 Uncertain significance (★).
Frequency
Consequence
NM_001184727.2 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 |
---|---|---|---|---|---|---|---|
GPRASP1 | NM_001184727.2 | c.1617G>T | p.Glu539Asp | missense_variant | 6/6 | ENST00000537097.2 | |
ARMCX5-GPRASP2 | NR_146584.3 | n.649+49877G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPRASP1 | ENST00000537097.2 | c.1617G>T | p.Glu539Asp | missense_variant | 6/6 | 2 | NM_001184727.2 | P1 | |
ENST00000602441.1 | n.57+4126C>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000270 AC: 3AN: 111303Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33499
GnomAD3 exomes AF: 0.0000708 AC: 13AN: 183506Hom.: 0 AF XY: 0.0000736 AC XY: 5AN XY: 67938
GnomAD4 exome AF: 0.0000200 AC: 22AN: 1098152Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 5AN XY: 363512
GnomAD4 genome ? AF: 0.0000269 AC: 3AN: 111358Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33564
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.1617G>T (p.E539D) alteration is located in exon 6 (coding exon 1) of the GPRASP1 gene. This alteration results from a G to T substitution at nucleotide position 1617, causing the glutamic acid (E) at amino acid position 539 to be replaced by an aspartic acid (D). 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