3-149767569-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001144960.3(ANKUB1):c.1093G>T(p.Ala365Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000709 in 1,551,548 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144960.3 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 |
---|---|---|---|---|---|---|---|
ANKUB1 | NM_001144960.3 | c.1093G>T | p.Ala365Ser | missense_variant | 5/6 | ENST00000446160.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKUB1 | ENST00000446160.7 | c.1093G>T | p.Ala365Ser | missense_variant | 5/6 | 5 | NM_001144960.3 | P1 | |
ANKUB1 | ENST00000484019.1 | c.*863G>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 1 | ||||
ANKUB1 | ENST00000462519.3 | c.1093G>T | p.Ala365Ser | missense_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000643 AC: 9AN: 1399402Hom.: 0 Cov.: 34 AF XY: 0.00000580 AC XY: 4AN XY: 690206
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2023 | The c.1093G>T (p.A365S) alteration is located in exon 5 (coding exon 5) of the ANKUB1 gene. This alteration results from a G to T substitution at nucleotide position 1093, causing the alanine (A) at amino acid position 365 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