2-170716659-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001003845.3(SP5):c.452C>G(p.Ala151Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000414 in 1,448,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001003845.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SP5 | NM_001003845.3 | c.452C>G | p.Ala151Gly | missense_variant | Exon 2 of 2 | ENST00000375281.4 | NP_001003845.1 | |
SP5 | XM_005246542.5 | c.584C>G | p.Ala195Gly | missense_variant | Exon 2 of 2 | XP_005246599.1 | ||
SP5 | XM_047444264.1 | c.224C>G | p.Ala75Gly | missense_variant | Exon 2 of 2 | XP_047300220.1 | ||
ERICH2-DT | NR_110185.1 | n.376+6845G>C | intron_variant | Intron 5 of 5 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1448202Hom.: 0 Cov.: 38 AF XY: 0.00000555 AC XY: 4AN XY: 720166
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.452C>G (p.A151G) alteration is located in exon 2 (coding exon 2) of the SP5 gene. This alteration results from a C to G substitution at nucleotide position 452, causing the alanine (A) at amino acid position 151 to be replaced by a glycine (G). 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
Publications
No publications associated with this variant yet.