1-213051475-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001287221.3(RPS6KC1):c.-352C>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 0.000152 in 1,613,494 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001287221.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS6KC1 | NM_012424.6 | c.71C>T | p.Pro24Leu | missense_variant | 1/15 | ENST00000366960.8 | NP_036556.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS6KC1 | ENST00000366960.8 | c.71C>T | p.Pro24Leu | missense_variant | 1/15 | 1 | NM_012424.6 | ENSP00000355927.3 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000248 AC: 61AN: 246354Hom.: 0 AF XY: 0.000202 AC XY: 27AN XY: 133858
GnomAD4 exome AF: 0.000148 AC: 216AN: 1461238Hom.: 1 Cov.: 31 AF XY: 0.000150 AC XY: 109AN XY: 726894
GnomAD4 genome AF: 0.000197 AC: 30AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 25, 2023 | The c.71C>T (p.P24L) alteration is located in exon 1 (coding exon 1) of the RPS6KC1 gene. This alteration results from a C to T substitution at nucleotide position 71, causing the proline (P) at amino acid position 24 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at