chr1-30874504-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014654.4(SDC3):c.955C>A(p.Leu319Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000142 in 1,614,054 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_014654.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDC3 | NM_014654.4 | c.955C>A | p.Leu319Met | missense_variant | Exon 4 of 5 | ENST00000339394.7 | NP_055469.3 | |
SDC3 | XM_011542463.1 | c.922C>A | p.Leu308Met | missense_variant | Exon 4 of 5 | XP_011540765.1 | ||
SDC3 | XM_011542464.3 | c.919C>A | p.Leu307Met | missense_variant | Exon 4 of 5 | XP_011540766.1 | ||
SDC3 | XM_011542466.2 | c.829C>A | p.Leu277Met | missense_variant | Exon 4 of 5 | XP_011540768.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDC3 | ENST00000339394.7 | c.955C>A | p.Leu319Met | missense_variant | Exon 4 of 5 | 1 | NM_014654.4 | ENSP00000344468.6 | ||
SDC3 | ENST00000336798.11 | c.781C>A | p.Leu261Met | missense_variant | Exon 2 of 3 | 1 | ENSP00000338346.7 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251456Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135900
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461854Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727238
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.955C>A (p.L319M) alteration is located in exon 4 (coding exon 4) of the SDC3 gene. This alteration results from a C to A substitution at nucleotide position 955, causing the leucine (L) at amino acid position 319 to be replaced by a methionine (M). 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