2-218217527-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_152862.3(ARPC2):c.57C>A(p.Phe19Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,126 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152862.3 missense
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 |
---|---|---|---|---|---|---|---|---|
ARPC2 | NM_152862.3 | c.57C>A | p.Phe19Leu | missense_variant | Exon 2 of 11 | ENST00000315717.10 | NP_690601.1 | |
ARPC2 | NM_005731.3 | c.57C>A | p.Phe19Leu | missense_variant | Exon 1 of 10 | NP_005722.1 | ||
ARPC2 | XM_017003113.2 | c.-92+273C>A | intron_variant | Intron 1 of 9 | XP_016858602.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000488 AC: 12AN: 245678Hom.: 0 AF XY: 0.0000671 AC XY: 9AN XY: 134148
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461028Hom.: 0 Cov.: 33 AF XY: 0.0000316 AC XY: 23AN XY: 726818
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.57C>A (p.F19L) alteration is located in exon 2 (coding exon 1) of the ARPC2 gene. This alteration results from a C to A substitution at nucleotide position 57, causing the phenylalanine (F) at amino acid position 19 to be replaced by a leucine (L). 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