X-1198571-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_022148.4(CRLF2):c.637G>A(p.Glu213Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000356 in 1,613,642 control chromosomes in the GnomAD database, including 4 homozygotes. There are 371 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRLF2 | NM_022148.4 | c.637G>A | p.Glu213Lys | missense_variant | 5/8 | ENST00000400841.8 | |
CRLF2 | NM_001012288.3 | c.301G>A | p.Glu101Lys | missense_variant | 4/7 | ||
CRLF2 | XM_011546181.3 | c.634G>A | p.Glu212Lys | missense_variant | 5/8 | ||
CRLF2 | NR_110830.2 | n.840+230G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRLF2 | ENST00000400841.8 | c.637G>A | p.Glu213Lys | missense_variant | 5/8 | 1 | NM_022148.4 | P1 | |
CRLF2 | ENST00000381567.8 | c.301G>A | p.Glu101Lys | missense_variant | 4/7 | 1 | |||
CRLF2 | ENST00000467626.6 | c.*126+230G>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152070Hom.: 0 Cov.: 30 AF XY: 0.000269 AC XY: 20AN XY: 74270
GnomAD3 exomes AF: 0.000643 AC: 160AN: 248818Hom.: 0 AF XY: 0.000837 AC XY: 113AN XY: 134958
GnomAD4 exome AF: 0.000369 AC: 540AN: 1461454Hom.: 4 Cov.: 39 AF XY: 0.000483 AC XY: 351AN XY: 727016
GnomAD4 genome AF: 0.000230 AC: 35AN: 152188Hom.: 0 Cov.: 30 AF XY: 0.000269 AC XY: 20AN XY: 74398
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