4-174975718-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_014269.4(ADAM29):c.193A>T(p.Ile65Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,611,932 control chromosomes in the GnomAD database, including 3 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_014269.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAM29 | NM_014269.4 | c.193A>T | p.Ile65Phe | missense_variant | 5/5 | ENST00000359240.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAM29 | ENST00000359240.7 | c.193A>T | p.Ile65Phe | missense_variant | 5/5 | 2 | NM_014269.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000828 AC: 126AN: 152128Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00106 AC: 264AN: 248484Hom.: 0 AF XY: 0.000991 AC XY: 133AN XY: 134272
GnomAD4 exome AF: 0.00105 AC: 1527AN: 1459686Hom.: 3 Cov.: 31 AF XY: 0.00103 AC XY: 749AN XY: 726076
GnomAD4 genome ? AF: 0.000828 AC: 126AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.000725 AC XY: 54AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.193A>T (p.I65F) alteration is located in exon 5 (coding exon 1) of the ADAM29 gene. This alteration results from a A to T substitution at nucleotide position 193, causing the isoleucine (I) at amino acid position 65 to be replaced by a phenylalanine (F). 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