chr2-233816781-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001394639.1(MROH2A):c.2857C>T(p.Leu953Phe) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00593 in 1,549,136 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001394639.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MROH2A | NM_001394639.1 | c.2857C>T | p.Leu953Phe | missense_variant, splice_region_variant | 27/42 | ENST00000389758.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MROH2A | ENST00000389758.4 | c.2857C>T | p.Leu953Phe | missense_variant, splice_region_variant | 27/42 | 5 | NM_001394639.1 | A2 | |
MROH2A | ENST00000610772.4 | c.2866C>T | p.Leu956Phe | missense_variant, splice_region_variant | 27/42 | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00434 AC: 661AN: 152226Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00419 AC: 623AN: 148748Hom.: 4 AF XY: 0.00419 AC XY: 336AN XY: 80136
GnomAD4 exome AF: 0.00611 AC: 8529AN: 1396792Hom.: 47 Cov.: 29 AF XY: 0.00581 AC XY: 4004AN XY: 688986
GnomAD4 genome ? AF: 0.00434 AC: 661AN: 152344Hom.: 3 Cov.: 33 AF XY: 0.00431 AC XY: 321AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | MROH2A: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at