rs4949184
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The ENST00000339394.7(SDC3):c.907G>T(p.Asp303Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,461,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D303N) has been classified as Likely benign.
Frequency
Consequence
ENST00000339394.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDC3 | NM_014654.4 | c.907G>T | p.Asp303Tyr | missense_variant | 4/5 | ENST00000339394.7 | NP_055469.3 | |
SDC3 | XM_011542463.1 | c.874G>T | p.Asp292Tyr | missense_variant | 4/5 | XP_011540765.1 | ||
SDC3 | XM_011542464.3 | c.871G>T | p.Asp291Tyr | missense_variant | 4/5 | XP_011540766.1 | ||
SDC3 | XM_011542466.2 | c.781G>T | p.Asp261Tyr | missense_variant | 4/5 | XP_011540768.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDC3 | ENST00000339394.7 | c.907G>T | p.Asp303Tyr | missense_variant | 4/5 | 1 | NM_014654.4 | ENSP00000344468 | P1 | |
SDC3 | ENST00000336798.11 | c.733G>T | p.Asp245Tyr | missense_variant | 2/3 | 1 | ENSP00000338346 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251266Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135802
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461834Hom.: 0 Cov.: 35 AF XY: 0.0000248 AC XY: 18AN XY: 727226
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at