X-139585133-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001171876.2(MCF2):c.2906C>T(p.Ala969Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000345 in 1,202,039 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 138 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001171876.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCF2 | NM_001171876.2 | c.2906C>T | p.Ala969Val | missense_variant | 28/29 | ENST00000519895.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCF2 | ENST00000519895.6 | c.2906C>T | p.Ala969Val | missense_variant | 28/29 | 2 | NM_001171876.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000189 AC: 21AN: 111269Hom.: 0 Cov.: 22 AF XY: 0.000239 AC XY: 8AN XY: 33489
GnomAD3 exomes AF: 0.000141 AC: 25AN: 177020Hom.: 0 AF XY: 0.000161 AC XY: 10AN XY: 62086
GnomAD4 exome AF: 0.000361 AC: 394AN: 1090770Hom.: 0 Cov.: 27 AF XY: 0.000364 AC XY: 130AN XY: 356950
GnomAD4 genome AF: 0.000189 AC: 21AN: 111269Hom.: 0 Cov.: 22 AF XY: 0.000239 AC XY: 8AN XY: 33489
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.2906C>T (p.A969V) alteration is located in exon 28 (coding exon 27) of the MCF2 gene. This alteration results from a C to T substitution at nucleotide position 2906, causing the alanine (A) at amino acid position 969 to be replaced by a valine (V). 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