chr7-92307489-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM2PP2BP4_StrongBP6_Moderate
The NM_019004.2(ANKIB1):āc.319A>Gā(p.Thr107Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_019004.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKIB1 | NM_019004.2 | c.319A>G | p.Thr107Ala | missense_variant | 3/20 | ENST00000265742.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKIB1 | ENST00000265742.8 | c.319A>G | p.Thr107Ala | missense_variant | 3/20 | 1 | NM_019004.2 | P1 | |
ANKIB1 | ENST00000442183.1 | c.319A>G | p.Thr107Ala | missense_variant | 3/3 | 4 | |||
ANKIB1 | ENST00000439883.1 | c.133A>G | p.Thr45Ala | missense_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249076Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135114
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461674Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727118
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | 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