21-36369010-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015358.3(MORC3):c.1642C>T(p.Arg548Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,609,486 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015358.3 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 |
---|---|---|---|---|---|---|---|
MORC3 | NM_015358.3 | c.1642C>T | p.Arg548Cys | missense_variant | 15/17 | ENST00000400485.6 | |
MORC3 | NM_001320445.2 | c.1429C>T | p.Arg477Cys | missense_variant | 14/16 | ||
MORC3 | NM_001320446.2 | c.1429C>T | p.Arg477Cys | missense_variant | 16/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MORC3 | ENST00000400485.6 | c.1642C>T | p.Arg548Cys | missense_variant | 15/17 | 1 | NM_015358.3 | P1 | |
MORC3 | ENST00000484028.1 | n.583C>T | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
MORC3 | ENST00000487909.5 | n.1603C>T | non_coding_transcript_exon_variant | 14/16 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152030Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000130 AC: 32AN: 247100Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 134168
GnomAD4 exome AF: 0.000161 AC: 235AN: 1457456Hom.: 0 Cov.: 30 AF XY: 0.000164 AC XY: 119AN XY: 724412
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152030Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.1642C>T (p.R548C) alteration is located in exon 15 (coding exon 15) of the MORC3 gene. This alteration results from a C to T substitution at nucleotide position 1642, causing the arginine (R) at amino acid position 548 to be replaced by a cysteine (C). 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