6-109441974-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003080.3(SMPD2):c.225C>T(p.Ser75Ser) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003080.3 splice_region, synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMPD2 | NM_003080.3 | c.225C>T | p.Ser75Ser | splice_region_variant, synonymous_variant | Exon 4 of 10 | ENST00000258052.8 | NP_003071.2 | |
SMPD2 | XM_011536079.2 | c.-91C>T | 5_prime_UTR_variant | Exon 2 of 8 | XP_011534381.1 | |||
SMPD2 | XR_942566.3 | n.623C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 4 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMPD2 | ENST00000258052.8 | c.225C>T | p.Ser75Ser | splice_region_variant, synonymous_variant | Exon 4 of 10 | 1 | NM_003080.3 | ENSP00000258052.3 | ||
SMPD2 | ENST00000439615.1 | n.27C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251468Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135902
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461470Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727074
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at