chr10-48184619-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001018071.4(FRMPD2):c.2531G>A(p.Arg844Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,782 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 Uncertain significance (★).
Frequency
Consequence
NM_001018071.4 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 |
---|---|---|---|---|---|---|---|
FRMPD2 | NM_001018071.4 | c.2531G>A | p.Arg844Lys | missense_variant | 20/29 | ENST00000374201.8 | |
FRMPD2 | NM_001318191.1 | c.2456G>A | p.Arg819Lys | missense_variant | 18/27 | ||
FRMPD2 | XM_047424652.1 | c.2528G>A | p.Arg843Lys | missense_variant | 20/22 | ||
FRMPD2 | XM_047424653.1 | c.2438G>A | p.Arg813Lys | missense_variant | 18/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRMPD2 | ENST00000374201.8 | c.2531G>A | p.Arg844Lys | missense_variant | 20/29 | 1 | NM_001018071.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251210Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135754
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461500Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727094
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.2531G>A (p.R844K) alteration is located in exon 20 (coding exon 20) of the FRMPD2 gene. This alteration results from a G to A substitution at nucleotide position 2531, causing the arginine (R) at amino acid position 844 to be replaced by a lysine (K). 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