16-1844960-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001163560.3(MEIOB):āc.782T>Cā(p.Ile261Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,412,474 control chromosomes in the GnomAD database, including 19,038 homozygotes. 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 Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001163560.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MEIOB | NM_001163560.3 | c.782T>C | p.Ile261Thr | missense_variant | 10/14 | ENST00000325962.9 | NP_001157032.1 | |
MEIOB | NM_152764.3 | c.782T>C | p.Ile261Thr | missense_variant | 10/13 | NP_689977.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MEIOB | ENST00000325962.9 | c.782T>C | p.Ile261Thr | missense_variant | 10/14 | 5 | NM_001163560.3 | ENSP00000314484 | P1 | |
ENST00000470044.5 | c.161T>C | p.Ile54Thr | missense_variant | 9/13 | 2 | ENSP00000457416 | P1 | |||
MEIOB | ENST00000397344.7 | c.782T>C | p.Ile261Thr | missense_variant | 10/13 | 5 | ENSP00000380504 | |||
MEIOB | ENST00000496541.6 | c.161T>C | p.Ter54= | incomplete_terminal_codon_variant, coding_sequence_variant | 8/8 | 5 | ENSP00000456880 |
Frequencies
GnomAD3 genomes AF: 0.178 AC: 27084AN: 152054Hom.: 2572 Cov.: 32
GnomAD3 exomes AF: 0.177 AC: 40380AN: 227970Hom.: 3871 AF XY: 0.182 AC XY: 22461AN XY: 123424
GnomAD4 exome AF: 0.155 AC: 195624AN: 1260300Hom.: 16465 Cov.: 17 AF XY: 0.160 AC XY: 100749AN XY: 629962
GnomAD4 genome AF: 0.178 AC: 27102AN: 152174Hom.: 2573 Cov.: 32 AF XY: 0.186 AC XY: 13845AN XY: 74386
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2019 | This variant is associated with the following publications: (PMID: 30679340) - |
MEIOB-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 23, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at