chr3-183193026-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015078.4(MCF2L2):c.2989C>T(p.Pro997Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015078.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCF2L2 | NM_015078.4 | c.2989C>T | p.Pro997Ser | missense_variant | 27/30 | ENST00000328913.8 | |
MCF2L2 | XM_011512585.3 | c.1930C>T | p.Pro644Ser | missense_variant | 19/22 | ||
MCF2L2 | XM_047447751.1 | c.1888C>T | p.Pro630Ser | missense_variant | 18/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCF2L2 | ENST00000328913.8 | c.2989C>T | p.Pro997Ser | missense_variant | 27/30 | 5 | NM_015078.4 | A2 | |
MCF2L2 | ENST00000473233.5 | c.2989C>T | p.Pro997Ser | missense_variant | 27/29 | 5 | P4 | ||
MCF2L2 | ENST00000468976.5 | n.370C>T | non_coding_transcript_exon_variant | 5/6 | 4 | ||||
MCF2L2 | ENST00000488149.5 | n.7436C>T | non_coding_transcript_exon_variant | 28/28 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461802Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727222
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | The c.2989C>T (p.P997S) alteration is located in exon 27 (coding exon 27) of the MCF2L2 gene. This alteration results from a C to T substitution at nucleotide position 2989, causing the proline (P) at amino acid position 997 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.