15-78811214-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014272.5(ADAMTS7):c.7G>A(p.Gly3Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000195 in 1,228,142 control chromosomes in the GnomAD database, including 1 homozygotes. 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_014272.5 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 |
---|---|---|---|---|---|---|---|
ADAMTS7 | NM_014272.5 | c.7G>A | p.Gly3Ser | missense_variant | 1/24 | ENST00000388820.5 | |
ADAMTS7 | XM_047432122.1 | c.7G>A | p.Gly3Ser | missense_variant | 1/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS7 | ENST00000388820.5 | c.7G>A | p.Gly3Ser | missense_variant | 1/24 | 1 | NM_014272.5 | P1 | |
MORF4L1 | ENST00000379535.8 | c.-10+173C>T | intron_variant | 2 | |||||
ADAMTS7 | ENST00000566303.5 | n.70G>A | non_coding_transcript_exon_variant | 1/10 | 5 | ||||
ADAMTS7 | ENST00000568712.1 | n.19G>A | non_coding_transcript_exon_variant | 1/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152044Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000929 AC: 10AN: 1075992Hom.: 1 Cov.: 31 AF XY: 0.00000197 AC XY: 1AN XY: 508046
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 31, 2023 | The c.7G>A (p.G3S) alteration is located in exon 1 (coding exon 1) of the ADAMTS7 gene. This alteration results from a G to A substitution at nucleotide position 7, causing the glycine (G) at amino acid position 3 to be replaced by a serine (S). 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