17-30793594-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015986.4(CRLF3):c.682G>A(p.Val228Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000116 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015986.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRLF3 | ENST00000324238.7 | c.682G>A | p.Val228Ile | missense_variant | Exon 5 of 8 | 1 | NM_015986.4 | ENSP00000318804.6 | ||
CRLF3 | ENST00000578692.1 | n.*183G>A | non_coding_transcript_exon_variant | Exon 4 of 7 | 2 | ENSP00000462643.1 | ||||
CRLF3 | ENST00000578692.1 | n.*183G>A | 3_prime_UTR_variant | Exon 4 of 7 | 2 | ENSP00000462643.1 | ||||
CRLF3 | ENST00000577725.1 | n.393-7103G>A | intron_variant | Intron 1 of 2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152128Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251472Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135910
GnomAD4 exome AF: 0.000120 AC: 175AN: 1461814Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 78AN XY: 727224
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152128Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.682G>A (p.V228I) alteration is located in exon 5 (coding exon 5) of the CRLF3 gene. This alteration results from a G to A substitution at nucleotide position 682, causing the valine (V) at amino acid position 228 to be replaced by an isoleucine (I). 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