rs587778219
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_022148.4(CRLF2):c.190G>A(p.Gly64Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,612,964 control chromosomes in the GnomAD database, including 1 homozygotes. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/17 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
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRLF2 | NM_022148.4 | c.190G>A | p.Gly64Ser | missense_variant | 3/8 | ENST00000400841.8 | |
CRLF2 | XM_011546181.3 | c.187G>A | p.Gly63Ser | missense_variant | 3/8 | ||
CRLF2 | NM_001012288.3 | c.-147G>A | 5_prime_UTR_variant | 2/7 | |||
CRLF2 | NR_110830.2 | n.202G>A | non_coding_transcript_exon_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRLF2 | ENST00000400841.8 | c.190G>A | p.Gly64Ser | missense_variant | 3/8 | 1 | NM_022148.4 | P1 | |
CRLF2 | ENST00000381567.8 | c.-147G>A | 5_prime_UTR_variant | 2/7 | 1 | ||||
CRLF2 | ENST00000467626.6 | c.187G>A | p.Gly63Ser | missense_variant, NMD_transcript_variant | 3/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74286
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248020Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134552
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1460768Hom.: 1 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726664
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74414
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