3-183179578-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015078.4(MCF2L2):āc.3220A>Gā(p.Thr1074Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,614,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/25 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015078.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCF2L2 | NM_015078.4 | c.3220A>G | p.Thr1074Ala | missense_variant, splice_region_variant | 29/30 | ENST00000328913.8 | |
MCF2L2 | XM_011512585.3 | c.2161A>G | p.Thr721Ala | missense_variant, splice_region_variant | 21/22 | ||
MCF2L2 | XM_047447751.1 | c.2119A>G | p.Thr707Ala | missense_variant, splice_region_variant | 20/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCF2L2 | ENST00000328913.8 | c.3220A>G | p.Thr1074Ala | missense_variant, splice_region_variant | 29/30 | 5 | NM_015078.4 | A2 | |
MCF2L2 | ENST00000473233.5 | c.3220A>G | p.Thr1074Ala | missense_variant | 29/29 | 5 | P4 | ||
MCF2L2 | ENST00000464626.1 | n.356A>G | non_coding_transcript_exon_variant | 2/2 | 4 | ||||
MCF2L2 | ENST00000478652.1 | n.358A>G | splice_region_variant, non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251028Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135736
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461786Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727200
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.3220A>G (p.T1074A) alteration is located in exon 29 (coding exon 29) of the MCF2L2 gene. This alteration results from a A to G substitution at nucleotide position 3220, causing the threonine (T) at amino acid position 1074 to be replaced by an alanine (A). 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