chr3-183206183-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015078.4(MCF2L2):āc.2744G>Cā(p.Arg915Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R915M) has been classified as Uncertain significance.
Frequency
Consequence
NM_015078.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCF2L2 | NM_015078.4 | c.2744G>C | p.Arg915Thr | missense_variant | 24/30 | ENST00000328913.8 | |
MCF2L2 | XM_017005943.3 | c.2744G>C | p.Arg915Thr | missense_variant | 24/26 | ||
MCF2L2 | XM_011512585.3 | c.1685G>C | p.Arg562Thr | missense_variant | 16/22 | ||
MCF2L2 | XM_047447751.1 | c.1643G>C | p.Arg548Thr | missense_variant | 15/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCF2L2 | ENST00000328913.8 | c.2744G>C | p.Arg915Thr | missense_variant | 24/30 | 5 | NM_015078.4 | A2 | |
MCF2L2 | ENST00000473233.5 | c.2744G>C | p.Arg915Thr | missense_variant | 24/29 | 5 | P4 | ||
MCF2L2 | ENST00000468976.5 | n.125G>C | non_coding_transcript_exon_variant | 2/6 | 4 | ||||
MCF2L2 | ENST00000488149.5 | n.7191G>C | non_coding_transcript_exon_variant | 25/28 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251370Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135854
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461850Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727230
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2023 | The c.2744G>C (p.R915T) alteration is located in exon 24 (coding exon 24) of the MCF2L2 gene. This alteration results from a G to C substitution at nucleotide position 2744, causing the arginine (R) at amino acid position 915 to be replaced by a threonine (T). 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