6-17130693-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001190766.2(STMND1):āc.643T>Cā(p.Phe215Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000013 in 1,535,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001190766.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STMND1 | NM_001190766.2 | c.643T>C | p.Phe215Leu | missense_variant | 5/5 | ENST00000536551.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STMND1 | ENST00000536551.6 | c.643T>C | p.Phe215Leu | missense_variant | 5/5 | 5 | NM_001190766.2 | P1 | |
STMND1 | ENST00000366215.2 | n.1406T>C | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
STMND1 | ENST00000354384.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32
GnomAD4 exome AF: 7.23e-7 AC: 1AN: 1383816Hom.: 0 Cov.: 31 AF XY: 0.00000146 AC XY: 1AN XY: 682846
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.643T>C (p.F215L) alteration is located in exon 5 (coding exon 5) of the STMND1 gene. This alteration results from a T to C substitution at nucleotide position 643, causing the phenylalanine (F) at amino acid position 215 to be replaced by a leucine (L). 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