rs4947012
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001329603.2(AK9):c.-612T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 320,516 control chromosomes in the GnomAD database, including 445 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001329603.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AK9 | ENST00000424296.7 | c.-12+76T>C | intron_variant | Intron 1 of 40 | 5 | NM_001145128.3 | ENSP00000410186.2 | |||
AK9 | ENST00000285397.9 | c.-12+76T>C | intron_variant | Intron 1 of 11 | 1 | ENSP00000285397.4 | ||||
AK9 | ENST00000368948.6 | c.-12+76T>C | intron_variant | Intron 1 of 19 | 5 | ENSP00000357944.2 | ||||
FIG4 | ENST00000675844.1 | c.-166+157A>G | intron_variant | Intron 1 of 7 | ENSP00000502353.1 |
Frequencies
GnomAD3 genomes AF: 0.0424 AC: 6444AN: 152118Hom.: 175 Cov.: 32
GnomAD4 exome AF: 0.0481 AC: 8088AN: 168280Hom.: 269 AF XY: 0.0495 AC XY: 4315AN XY: 87196
GnomAD4 genome AF: 0.0424 AC: 6459AN: 152236Hom.: 176 Cov.: 32 AF XY: 0.0421 AC XY: 3132AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at