chr2-170966015-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015530.5(GORASP2):c.1244C>T(p.Thr415Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,613,618 control chromosomes in the GnomAD database, including 34 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_015530.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GORASP2 | NM_015530.5 | c.1244C>T | p.Thr415Met | missense_variant | 10/10 | ENST00000234160.5 | |
GORASP2 | NM_001201428.2 | c.1040C>T | p.Thr347Met | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GORASP2 | ENST00000234160.5 | c.1244C>T | p.Thr415Met | missense_variant | 10/10 | 1 | NM_015530.5 | P1 | |
GORASP2 | ENST00000486498.1 | n.1510C>T | non_coding_transcript_exon_variant | 5/5 | 2 | ||||
GORASP2 | ENST00000442798.5 | c.*1276C>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00796 AC: 1211AN: 152104Hom.: 17 Cov.: 32
GnomAD3 exomes AF: 0.00223 AC: 561AN: 251298Hom.: 4 AF XY: 0.00156 AC XY: 212AN XY: 135852
GnomAD4 exome AF: 0.000807 AC: 1179AN: 1461396Hom.: 17 Cov.: 33 AF XY: 0.000690 AC XY: 502AN XY: 727044
GnomAD4 genome ? AF: 0.00797 AC: 1213AN: 152222Hom.: 17 Cov.: 32 AF XY: 0.00787 AC XY: 586AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at