21-14582274-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001395858.1(SAMSN1):c.903G>A(p.Lys301Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,550,730 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.
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000064 ( 0 hom. )
Consequence
SAMSN1
NM_001395858.1 synonymous
NM_001395858.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0950
Genes affected
SAMSN1 (HGNC:10528): (SAM domain, SH3 domain and nuclear localization signals 1) SAMSN1 is a member of a novel gene family of putative adaptors and scaffold proteins containing SH3 and SAM (sterile alpha motif) domains (Claudio et al., 2001 [PubMed 11536050]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP7
Synonymous conserved (PhyloP=-0.095 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SAMSN1 | NM_001395858.1 | c.903G>A | p.Lys301Lys | synonymous_variant | Exon 11 of 18 | NP_001382787.1 | ||
| SAMSN1 | NM_001395857.1 | c.807G>A | p.Lys269Lys | synonymous_variant | Exon 9 of 16 | NP_001382786.1 | ||
| SAMSN1 | NM_001256370.2 | c.123G>A | p.Lys41Lys | synonymous_variant | Exon 2 of 9 | NP_001243299.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SAMSN1 | ENST00000285670.7 | c.123G>A | p.Lys41Lys | synonymous_variant | Exon 2 of 9 | 1 | ENSP00000285670.2 | |||
| SAMSN1 | ENST00000647101.1 | c.807G>A | p.Lys269Lys | synonymous_variant | Exon 9 of 16 | ENSP00000493867.1 | ||||
| SAMSN1-AS1 | ENST00000449214.1 | n.73C>T | non_coding_transcript_exon_variant | Exon 1 of 5 | 3 | |||||
| SAMSN1 | ENST00000644288.1 | n.298G>A | non_coding_transcript_exon_variant | Exon 2 of 9 |
Frequencies
GnomAD3 genomes 0.0000526 AC: 8AN: 152196Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000133 AC: 2AN: 150508Hom.: 0 AF XY: 0.0000124 AC XY: 1AN XY: 80768
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GnomAD4 exome AF: 0.00000644 AC: 9AN: 1398534Hom.: 0 Cov.: 40 AF XY: 0.00000435 AC XY: 3AN XY: 689786
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GnomAD4 genome 0.0000526 AC: 8AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at