12-56273097-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_004077.3(CS):c.1388C>T(p.Ser463Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00203 in 1,609,866 control chromosomes in the GnomAD database, including 7 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_004077.3 missense
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 |
---|---|---|---|---|---|---|---|---|
CS | NM_004077.3 | c.1388C>T | p.Ser463Phe | missense_variant | Exon 11 of 11 | ENST00000351328.8 | NP_004068.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00149 AC: 226AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00149 AC: 365AN: 245748Hom.: 1 AF XY: 0.00163 AC XY: 217AN XY: 132804
GnomAD4 exome AF: 0.00209 AC: 3050AN: 1457630Hom.: 7 Cov.: 31 AF XY: 0.00212 AC XY: 1536AN XY: 724892
GnomAD4 genome AF: 0.00148 AC: 225AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.00132 AC XY: 98AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1388C>T (p.S463F) alteration is located in exon 11 (coding exon 11) of the CS gene. This alteration results from a C to T substitution at nucleotide position 1388, causing the serine (S) at amino acid position 463 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at