5-75590351-A-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_ModerateBS1BS2
The NM_001387110.3(POLK):c.1260-2A>C variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.00087 in 1,573,402 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001387110.3 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLK | NM_001387111.3 | c.1309A>C | p.Ser437Arg | missense_variant | Exon 12 of 16 | NP_001374040.1 | ||
POLK | NM_001395894.1 | c.1309A>C | p.Ser437Arg | missense_variant | Exon 13 of 17 | NP_001382823.1 | ||
POLK | NM_001395897.1 | c.1306A>C | p.Ser436Arg | missense_variant | Exon 12 of 16 | NP_001382826.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00465 AC: 707AN: 152198Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00130 AC: 312AN: 239804Hom.: 6 AF XY: 0.000877 AC XY: 114AN XY: 129936
GnomAD4 exome AF: 0.000465 AC: 661AN: 1421086Hom.: 9 Cov.: 25 AF XY: 0.000417 AC XY: 295AN XY: 707390
GnomAD4 genome AF: 0.00465 AC: 708AN: 152316Hom.: 5 Cov.: 32 AF XY: 0.00431 AC XY: 321AN XY: 74486
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at