rs2274755
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_004994.3(MMP9):c.649+3G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,613,514 control chromosomes in the GnomAD database, including 20,020 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004994.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.154 AC: 23398AN: 152084Hom.: 1885 Cov.: 33
GnomAD3 exomes AF: 0.154 AC: 38552AN: 250870Hom.: 3437 AF XY: 0.163 AC XY: 22093AN XY: 135676
GnomAD4 exome AF: 0.152 AC: 222093AN: 1461312Hom.: 18137 Cov.: 44 AF XY: 0.157 AC XY: 113780AN XY: 726998
GnomAD4 genome AF: 0.154 AC: 23415AN: 152202Hom.: 1883 Cov.: 33 AF XY: 0.155 AC XY: 11565AN XY: 74410
ClinVar
Submissions by phenotype
Metaphyseal anadysplasia 2 Benign:3
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
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not provided Benign:3
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This variant is associated with the following publications: (PMID: 16631427, 25525159) -
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at