rs587778218
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_022148.4(CRLF2):c.269A>G(p.Gln90Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,613,572 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_022148.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRLF2 | NM_022148.4 | c.269A>G | p.Gln90Arg | missense_variant | 3/8 | ENST00000400841.8 | |
CRLF2 | XM_011546181.3 | c.266A>G | p.Gln89Arg | missense_variant | 3/8 | ||
CRLF2 | NM_001012288.3 | c.-68A>G | 5_prime_UTR_variant | 2/7 | |||
CRLF2 | NR_110830.2 | n.281A>G | non_coding_transcript_exon_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRLF2 | ENST00000400841.8 | c.269A>G | p.Gln90Arg | missense_variant | 3/8 | 1 | NM_022148.4 | P1 | |
CRLF2 | ENST00000381567.8 | c.-68A>G | 5_prime_UTR_variant | 2/7 | 1 | ||||
CRLF2 | ENST00000467626.6 | c.266A>G | p.Gln89Arg | missense_variant, NMD_transcript_variant | 3/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248962Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135050
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461386Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726984
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at