chr21-36369252-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015358.3(MORC3):c.1884A>G(p.Ser628=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 1,614,220 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00018 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00032 ( 6 hom. )
Consequence
MORC3
NM_015358.3 synonymous
NM_015358.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.53
Genes affected
MORC3 (HGNC:23572): (MORC family CW-type zinc finger 3) This gene encodes a protein that localizes to the nuclear matrix and forms nuclear bodies via an ATP-dependent mechanism. The protein is predicted to have coiled-coil and zinc finger domains and has RNA binding activity. Alternative splicing produces multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 21-36369252-A-G is Benign according to our data. Variant chr21-36369252-A-G is described in ClinVar as [Benign]. Clinvar id is 773090.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.53 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MORC3 | NM_015358.3 | c.1884A>G | p.Ser628= | synonymous_variant | 15/17 | ENST00000400485.6 | |
MORC3 | NM_001320445.2 | c.1671A>G | p.Ser557= | synonymous_variant | 14/16 | ||
MORC3 | NM_001320446.2 | c.1671A>G | p.Ser557= | synonymous_variant | 16/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MORC3 | ENST00000400485.6 | c.1884A>G | p.Ser628= | synonymous_variant | 15/17 | 1 | NM_015358.3 | P1 | |
MORC3 | ENST00000487909.5 | n.1845A>G | non_coding_transcript_exon_variant | 14/16 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152208Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000725 AC: 181AN: 249564Hom.: 2 AF XY: 0.000916 AC XY: 124AN XY: 135398
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GnomAD4 exome AF: 0.000321 AC: 469AN: 1461894Hom.: 6 Cov.: 32 AF XY: 0.000439 AC XY: 319AN XY: 727248
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at