NM_003943.5:c.52C>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003943.5(STBD1):c.52C>A(p.Leu18Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,612,430 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003943.5 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: 0.0000329 AC: 5AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000566 AC: 14AN: 247204Hom.: 0 AF XY: 0.0000671 AC XY: 9AN XY: 134160
GnomAD4 exome AF: 0.0000288 AC: 42AN: 1460346Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 726524
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.52C>A (p.L18I) alteration is located in exon 1 (coding exon 1) of the STBD1 gene. This alteration results from a C to A substitution at nucleotide position 52, causing the leucine (L) at amino acid position 18 to be replaced by an isoleucine (I). 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