X-119539766-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_022101.4(STEEP1):c.630G>A(p.Ala210Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000572 in 1,205,943 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 23 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_022101.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STEEP1 | NM_022101.4 | c.630G>A | p.Ala210Ala | synonymous_variant | Exon 7 of 7 | ENST00000644802.2 | NP_071384.1 | |
STEEP1 | NM_001170570.2 | c.588G>A | p.Ala196Ala | synonymous_variant | Exon 6 of 6 | NP_001164041.1 | ||
STEEP1 | NM_001170569.1 | c.483G>A | p.Ala161Ala | synonymous_variant | Exon 7 of 7 | NP_001164040.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000542 AC: 6AN: 110781Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 32975
GnomAD3 exomes AF: 0.0000219 AC: 4AN: 182647Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67173
GnomAD4 exome AF: 0.0000575 AC: 63AN: 1095162Hom.: 0 Cov.: 27 AF XY: 0.0000638 AC XY: 23AN XY: 360594
GnomAD4 genome AF: 0.0000542 AC: 6AN: 110781Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 32975
ClinVar
Submissions by phenotype
not provided Benign:1
STEEP1: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at