chr16-81043621-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015251.3(ATMIN):c.1123A>C(p.Ile375Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00035 in 1,614,160 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015251.3 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 |
---|---|---|---|---|---|---|---|
ATMIN | NM_015251.3 | c.1123A>C | p.Ile375Leu | missense_variant | 4/4 | ENST00000299575.5 | |
ATMIN | NM_001300728.2 | c.655A>C | p.Ile219Leu | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATMIN | ENST00000299575.5 | c.1123A>C | p.Ile375Leu | missense_variant | 4/4 | 1 | NM_015251.3 | P1 | |
ATMIN | ENST00000564241.5 | c.655A>C | p.Ile219Leu | missense_variant | 4/4 | 1 | |||
ATMIN | ENST00000566488.1 | c.655A>C | p.Ile219Leu | missense_variant | 3/3 | 1 | |||
ATMIN | ENST00000539819.5 | n.881A>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000338 AC: 85AN: 251214Hom.: 0 AF XY: 0.000339 AC XY: 46AN XY: 135804
GnomAD4 exome AF: 0.000358 AC: 523AN: 1461878Hom.: 1 Cov.: 32 AF XY: 0.000385 AC XY: 280AN XY: 727242
GnomAD4 genome ? AF: 0.000276 AC: 42AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2023 | The c.1123A>C (p.I375L) alteration is located in exon 4 (coding exon 4) of the ATMIN gene. This alteration results from a A to C substitution at nucleotide position 1123, causing the isoleucine (I) at amino acid position 375 to be replaced by a leucine (L). 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