2-170961734-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015530.5(GORASP2):c.895G>C(p.Ala299Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000917 in 1,569,832 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_015530.5 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 |
---|---|---|---|---|---|---|---|
GORASP2 | NM_015530.5 | c.895G>C | p.Ala299Pro | missense_variant | 8/10 | ENST00000234160.5 | |
GORASP2 | NM_001201428.2 | c.691G>C | p.Ala231Pro | missense_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GORASP2 | ENST00000234160.5 | c.895G>C | p.Ala299Pro | missense_variant | 8/10 | 1 | NM_015530.5 | P1 | |
GORASP2 | ENST00000486498.1 | n.1161G>C | non_coding_transcript_exon_variant | 3/5 | 2 | ||||
GORASP2 | ENST00000493692.5 | n.726G>C | non_coding_transcript_exon_variant | 6/8 | 5 | ||||
GORASP2 | ENST00000442798.5 | c.*927G>C | 3_prime_UTR_variant, NMD_transcript_variant | 9/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000453 AC: 69AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251474Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135910
GnomAD4 exome AF: 0.0000529 AC: 75AN: 1417538Hom.: 0 Cov.: 24 AF XY: 0.0000452 AC XY: 32AN XY: 708012
GnomAD4 genome ? AF: 0.000453 AC: 69AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.000470 AC XY: 35AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.895G>C (p.A299P) alteration is located in exon 8 (coding exon 8) of the GORASP2 gene. This alteration results from a G to C substitution at nucleotide position 895, causing the alanine (A) at amino acid position 299 to be replaced by a proline (P). 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