chr3-183207739-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015078.4(MCF2L2):c.2581G>A(p.Asp861Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000867 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
MCF2L2
NM_015078.4 missense
NM_015078.4 missense
Scores
1
10
8
Clinical Significance
Conservation
PhyloP100: 6.68
Genes affected
MCF2L2 (HGNC:30319): (MCF.2 cell line derived transforming sequence-like 2) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of catalytic activity. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCF2L2 | NM_015078.4 | c.2581G>A | p.Asp861Asn | missense_variant | 23/30 | ENST00000328913.8 | |
MCF2L2 | XM_017005943.3 | c.2581G>A | p.Asp861Asn | missense_variant | 23/26 | ||
MCF2L2 | XM_011512585.3 | c.1522G>A | p.Asp508Asn | missense_variant | 15/22 | ||
MCF2L2 | XM_047447751.1 | c.1480G>A | p.Asp494Asn | missense_variant | 14/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCF2L2 | ENST00000328913.8 | c.2581G>A | p.Asp861Asn | missense_variant | 23/30 | 5 | NM_015078.4 | A2 | |
MCF2L2 | ENST00000473233.5 | c.2581G>A | p.Asp861Asn | missense_variant | 23/29 | 5 | P4 | ||
MCF2L2 | ENST00000488149.5 | n.7028G>A | non_coding_transcript_exon_variant | 24/28 | 2 | ||||
MCF2L2 | ENST00000468976.5 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251290Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135804
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GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461870Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727240
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.2581G>A (p.D861N) alteration is located in exon 23 (coding exon 23) of the MCF2L2 gene. This alteration results from a G to A substitution at nucleotide position 2581, causing the aspartic acid (D) at amino acid position 861 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Gain of MoRF binding (P = 0.0728);Gain of MoRF binding (P = 0.0728);
MVP
MPC
ClinPred
D
GERP RS
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Splicing
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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