17-28661818-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006923.4(SDF2):c.59G>A(p.Ser20Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict 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. S20T) has been classified as Uncertain significance.
Frequency
Consequence
NM_006923.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDF2 | NM_006923.4 | c.59G>A | p.Ser20Asn | missense_variant | Exon 1 of 3 | ENST00000247020.9 | NP_008854.2 | |
SDF2 | XM_011525106.3 | c.59G>A | p.Ser20Asn | missense_variant | Exon 2 of 5 | XP_011523408.1 | ||
SDF2 | XM_047436516.1 | c.59G>A | p.Ser20Asn | missense_variant | Exon 2 of 4 | XP_047292472.1 | ||
SDF2 | NR_045585.2 | n.149+228G>A | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251424Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135904
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727240
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at