rs17435959
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002425.3(MMP10):c.10C>G(p.Leu4Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 1,613,382 control chromosomes in the GnomAD database, including 2,113 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002425.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP10 | NM_002425.3 | c.10C>G | p.Leu4Val | missense_variant | 1/10 | ENST00000279441.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP10 | ENST00000279441.9 | c.10C>G | p.Leu4Val | missense_variant | 1/10 | 1 | NM_002425.3 | P1 | |
WTAPP1 | ENST00000371455.7 | n.325-17442G>C | intron_variant, non_coding_transcript_variant | 4 | |||||
MMP10 | ENST00000539681.1 | c.10C>G | p.Leu4Val | missense_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0712 AC: 10835AN: 152116Hom.: 618 Cov.: 32
GnomAD3 exomes AF: 0.0463 AC: 11592AN: 250474Hom.: 416 AF XY: 0.0447 AC XY: 6048AN XY: 135350
GnomAD4 exome AF: 0.0383 AC: 55970AN: 1461148Hom.: 1492 Cov.: 30 AF XY: 0.0383 AC XY: 27808AN XY: 726836
GnomAD4 genome ? AF: 0.0713 AC: 10855AN: 152234Hom.: 621 Cov.: 32 AF XY: 0.0711 AC XY: 5289AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2021 | This variant is associated with the following publications: (PMID: 26419737) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at