chr11-102791492-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002421.4(MMP1):c.1037A>C(p.Asn346Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,612,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002421.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP1 | NM_002421.4 | c.1037A>C | p.Asn346Thr | missense_variant | 8/10 | ENST00000315274.7 | |
WTAPP1 | NR_038390.1 | n.390-1653T>G | intron_variant, non_coding_transcript_variant | ||||
MMP1 | NM_001145938.2 | c.839A>C | p.Asn280Thr | missense_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP1 | ENST00000315274.7 | c.1037A>C | p.Asn346Thr | missense_variant | 8/10 | 1 | NM_002421.4 | P1 | |
WTAPP1 | ENST00000371455.7 | n.325-6532T>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000844 AC: 21AN: 248854Hom.: 0 AF XY: 0.0000893 AC XY: 12AN XY: 134404
GnomAD4 exome AF: 0.000116 AC: 170AN: 1459838Hom.: 0 Cov.: 31 AF XY: 0.000125 AC XY: 91AN XY: 726094
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.1037A>C (p.N346T) alteration is located in exon 8 (coding exon 8) of the MMP1 gene. This alteration results from a A to C substitution at nucleotide position 1037, causing the asparagine (N) at amino acid position 346 to be replaced by a threonine (T). 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