chr3-169926668-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001304366.2(SAMD7):c.406C>T(p.Pro136Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001304366.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAMD7 | NM_001304366.2 | c.406C>T | p.Pro136Ser | missense_variant | Exon 6 of 9 | ENST00000335556.7 | NP_001291295.1 | |
SAMD7 | NM_182610.4 | c.406C>T | p.Pro136Ser | missense_variant | Exon 6 of 9 | NP_872416.1 | ||
SAMD7 | NR_130713.2 | n.885C>T | non_coding_transcript_exon_variant | Exon 7 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAMD7 | ENST00000335556.7 | c.406C>T | p.Pro136Ser | missense_variant | Exon 6 of 9 | 1 | NM_001304366.2 | ENSP00000334668.3 | ||
SAMD7 | ENST00000428432.6 | c.406C>T | p.Pro136Ser | missense_variant | Exon 6 of 9 | 1 | ENSP00000391299.2 | |||
SAMD7 | ENST00000487910.1 | n.*222C>T | non_coding_transcript_exon_variant | Exon 6 of 9 | 1 | ENSP00000420460.1 | ||||
SAMD7 | ENST00000487910.1 | n.*222C>T | 3_prime_UTR_variant | Exon 6 of 9 | 1 | ENSP00000420460.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251356Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135892
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727232
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.406C>T (p.P136S) alteration is located in exon 6 (coding exon 4) of the SAMD7 gene. This alteration results from a C to T substitution at nucleotide position 406, causing the proline (P) at amino acid position 136 to be replaced by a serine (S). 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