chr8-2951126-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033225.6(CSMD1):āc.10189C>Gā(p.Leu3397Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,612,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_033225.6 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 |
---|---|---|---|---|---|---|---|
CSMD1 | NM_033225.6 | c.10189C>G | p.Leu3397Val | missense_variant | 66/70 | ENST00000635120.2 | |
LOC105377785 | NR_168443.1 | n.1172-57442G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSMD1 | ENST00000635120.2 | c.10189C>G | p.Leu3397Val | missense_variant | 66/70 | 5 | NM_033225.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 247748Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134372
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460622Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726574
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74430
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.10189C>G (p.L3397V) alteration is located in exon 66 (coding exon 66) of the CSMD1 gene. This alteration results from a C to G substitution at nucleotide position 10189, causing the leucine (L) at amino acid position 3397 to be replaced by a valine (V). 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