rs367657189
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_182895.5(SCARF2):āc.2579G>Cā(p.Arg860Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000783 in 1,276,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R860K) has been classified as Uncertain significance.
Frequency
Consequence
NM_182895.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCARF2 | NM_182895.5 | c.2579G>C | p.Arg860Thr | missense_variant | Exon 11 of 11 | ENST00000622235.5 | NP_878315.2 | |
SCARF2 | NM_153334.7 | c.2594G>C | p.Arg865Thr | missense_variant | Exon 11 of 11 | NP_699165.3 | ||
SCARF2 | XM_047441585.1 | c.2693G>C | p.Arg898Thr | missense_variant | Exon 11 of 11 | XP_047297541.1 | ||
SCARF2 | XM_017029065.3 | c.*808G>C | 3_prime_UTR_variant | Exon 11 of 11 | XP_016884554.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCARF2 | ENST00000622235.5 | c.2579G>C | p.Arg860Thr | missense_variant | Exon 11 of 11 | 1 | NM_182895.5 | ENSP00000477564.2 | ||
SCARF2 | ENST00000623402.1 | c.2594G>C | p.Arg865Thr | missense_variant | Exon 11 of 11 | 1 | ENSP00000485276.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.83e-7 AC: 1AN: 1276408Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 626466
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at