9-136952994-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_178536.4(LCN12):c.217G>A(p.Asp73Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000595 in 1,613,966 control chromosomes in the GnomAD database, including 2 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 Likely benign (★).
Frequency
Consequence
NM_178536.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCN12 | NM_178536.4 | c.217G>A | p.Asp73Asn | missense_variant | 2/6 | ENST00000371633.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCN12 | ENST00000371633.8 | c.217G>A | p.Asp73Asn | missense_variant | 2/6 | 1 | NM_178536.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000321 AC: 80AN: 249240Hom.: 0 AF XY: 0.000414 AC XY: 56AN XY: 135320
GnomAD4 exome AF: 0.000617 AC: 902AN: 1461714Hom.: 2 Cov.: 39 AF XY: 0.000611 AC XY: 444AN XY: 727186
GnomAD4 genome AF: 0.000381 AC: 58AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.000350 AC XY: 26AN XY: 74390
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at