NM_016240.3:c.83C>T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016240.3(SCARA3):c.83C>T(p.Pro28Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000805 in 1,613,972 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 Uncertain significance (★).
Frequency
Consequence
NM_016240.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 40AN: 251028Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135664
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461790Hom.: 0 Cov.: 31 AF XY: 0.0000798 AC XY: 58AN XY: 727192
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.83C>T (p.P28L) alteration is located in exon 2 (coding exon 2) of the SCARA3 gene. This alteration results from a C to T substitution at nucleotide position 83, causing the proline (P) at amino acid position 28 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
SCARA3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at