chr6-17129171-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001190766.2(STMND1):āc.471C>Gā(p.Ile157Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,535,822 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STMND1 | NM_001190766.2 | c.471C>G | p.Ile157Met | missense_variant | 4/5 | ENST00000536551.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STMND1 | ENST00000536551.6 | c.471C>G | p.Ile157Met | missense_variant | 4/5 | 5 | NM_001190766.2 | P1 | |
STMND1 | ENST00000354384.5 | c.447C>G | p.Ile149Met | missense_variant | 4/5 | 5 | |||
STMND1 | ENST00000366215.2 | n.1234C>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152014Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000238 AC: 32AN: 134598Hom.: 1 AF XY: 0.000246 AC XY: 18AN XY: 73300
GnomAD4 exome AF: 0.000159 AC: 220AN: 1383690Hom.: 2 Cov.: 30 AF XY: 0.000154 AC XY: 105AN XY: 682778
GnomAD4 genome AF: 0.000125 AC: 19AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.471C>G (p.I157M) alteration is located in exon 4 (coding exon 4) of the STMND1 gene. This alteration results from a C to G substitution at nucleotide position 471, causing the isoleucine (I) at amino acid position 157 to be replaced by a methionine (M). 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