chr11-627133-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021920.4(SCT):c.11G>A(p.Arg4Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000567 in 289,482 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R4W) has been classified as Uncertain significance.
Frequency
Consequence
NM_021920.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000656 AC: 9AN: 137184Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00102 AC: 155AN: 152298Hom.: 0 Cov.: 4 AF XY: 0.00102 AC XY: 76AN XY: 74414
GnomAD4 genome AF: 0.0000656 AC: 9AN: 137184Hom.: 0 Cov.: 31 AF XY: 0.0000749 AC XY: 5AN XY: 66712
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.11G>A (p.R4Q) alteration is located in exon 1 (coding exon 1) of the SCT gene. This alteration results from a G to A substitution at nucleotide position 11, causing the arginine (R) at amino acid position 4 to be replaced by a glutamine (Q). 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