chr17-50166018-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000023.4(SGCA):c.-23C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,609,794 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 Likely benign (★).
Frequency
Consequence
NM_000023.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SGCA | NM_000023.4 | c.-23C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | ENST00000262018.8 | NP_000014.1 | ||
SGCA | NM_000023.4 | c.-23C>T | 5_prime_UTR_variant | Exon 1 of 10 | ENST00000262018.8 | NP_000014.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SGCA | ENST00000262018 | c.-23C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | 1 | NM_000023.4 | ENSP00000262018.3 | |||
SGCA | ENST00000262018 | c.-23C>T | 5_prime_UTR_variant | Exon 1 of 10 | 1 | NM_000023.4 | ENSP00000262018.3 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247786Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134346
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1457500Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 725338
GnomAD4 genome AF: 0.000125 AC: 19AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at