chr19-48714898-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130915.2(MAMSTR):c.436T>C(p.Ser146Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,603,806 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130915.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAMSTR | NM_001130915.2 | c.436T>C | p.Ser146Pro | missense_variant | 6/10 | ENST00000318083.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAMSTR | ENST00000318083.11 | c.436T>C | p.Ser146Pro | missense_variant | 6/10 | 2 | NM_001130915.2 | P2 | |
MAMSTR | ENST00000594582.1 | c.127T>C | p.Ser43Pro | missense_variant | 4/7 | 1 | |||
MAMSTR | ENST00000356751.8 | c.127T>C | p.Ser43Pro | missense_variant | 4/8 | 2 | A2 | ||
MAMSTR | ENST00000599703.1 | c.586T>C | p.Ser196Pro | missense_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000264 AC: 40AN: 151476Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000232 AC: 57AN: 245958Hom.: 0 AF XY: 0.000301 AC XY: 40AN XY: 132908
GnomAD4 exome AF: 0.000158 AC: 229AN: 1452212Hom.: 1 Cov.: 32 AF XY: 0.000172 AC XY: 124AN XY: 722590
GnomAD4 genome ? AF: 0.000264 AC: 40AN: 151594Hom.: 0 Cov.: 30 AF XY: 0.000230 AC XY: 17AN XY: 74010
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2021 | The c.436T>C (p.S146P) alteration is located in exon 6 (coding exon 5) of the MAMSTR gene. This alteration results from a T to C substitution at nucleotide position 436, causing the serine (S) at amino acid position 146 to be replaced by a proline (P). 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