18-54224415-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_003927.5(MBD2):c.145G>T(p.Val49Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000724 in 1,243,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003927.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MBD2 | NM_003927.5 | c.145G>T | p.Val49Leu | missense_variant | 1/7 | ENST00000256429.8 | NP_003918.1 | |
MBD2 | NM_015832.6 | c.145G>T | p.Val49Leu | missense_variant | 1/3 | NP_056647.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MBD2 | ENST00000256429.8 | c.145G>T | p.Val49Leu | missense_variant | 1/7 | 1 | NM_003927.5 | ENSP00000256429.3 | ||
MBD2 | ENST00000583046.1 | c.145G>T | p.Val49Leu | missense_variant | 1/3 | 1 | ENSP00000464554.1 | |||
MBD2 | ENST00000398398.6 | c.145G>T | p.Val49Leu | missense_variant | 1/3 | 2 | ENSP00000381435.2 |
Frequencies
GnomAD3 genomes AF: 0.00000669 AC: 1AN: 149374Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000731 AC: 8AN: 1094260Hom.: 0 Cov.: 32 AF XY: 0.00000952 AC XY: 5AN XY: 525096
GnomAD4 genome AF: 0.00000669 AC: 1AN: 149374Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 72876
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2021 | The c.145G>T (p.V49L) alteration is located in exon 1 (coding exon 1) of the MBD2 gene. This alteration results from a G to T substitution at nucleotide position 145, causing the valine (V) at amino acid position 49 to be replaced by a leucine (L). 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