19-48744467-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_182575.3(IZUMO1):c.383G>T(p.Arg128Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182575.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IZUMO1 | NM_182575.3 | c.383G>T | p.Arg128Leu | missense_variant | Exon 4 of 10 | ENST00000332955.7 | NP_872381.2 | |
IZUMO1 | NM_001321864.1 | c.44G>T | p.Arg15Leu | missense_variant | Exon 3 of 9 | NP_001308793.1 | ||
IZUMO1 | NM_001321865.1 | c.-177G>T | 5_prime_UTR_variant | Exon 3 of 9 | NP_001308794.1 | |||
IZUMO1 | NR_135832.1 | n.389G>T | non_coding_transcript_exon_variant | Exon 3 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251464Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135898
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460942Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726842
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.383G>T (p.R128L) alteration is located in exon 4 (coding exon 3) of the IZUMO1 gene. This alteration results from a G to T substitution at nucleotide position 383, causing the arginine (R) at amino acid position 128 to be replaced by a leucine (L). 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