6-97181983-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001350599.2(MMS22L):āc.2305A>Gā(p.Ile769Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,613,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001350599.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMS22L | NM_001350599.2 | c.2305A>G | p.Ile769Val | missense_variant | 16/25 | ENST00000683635.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMS22L | ENST00000683635.1 | c.2305A>G | p.Ile769Val | missense_variant | 16/25 | NM_001350599.2 | P1 | ||
MMS22L | ENST00000275053.8 | c.2305A>G | p.Ile769Val | missense_variant | 16/25 | 2 | P1 | ||
MMS22L | ENST00000369251.6 | c.2185A>G | p.Ile729Val | missense_variant | 14/23 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251212Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135770
GnomAD4 exome AF: 0.0000629 AC: 92AN: 1461576Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 727080
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 07, 2022 | The c.2305A>G (p.I769V) alteration is located in exon 16 (coding exon 15) of the MMS22L gene. This alteration results from a A to G substitution at nucleotide position 2305, causing the isoleucine (I) at amino acid position 769 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