11-94307241-A-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001199206.4(IZUMO1R):āc.425A>Cā(p.Asp142Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000046 in 152,158 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000046 ( 0 hom., cov: 32)
Consequence
IZUMO1R
NM_001199206.4 missense
NM_001199206.4 missense
Scores
1
1
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.82
Genes affected
IZUMO1R (HGNC:32565): (IZUMO1 receptor, JUNO) Enables signaling receptor activity. Predicted to be involved in cell adhesion; fusion of sperm to egg plasma membrane involved in single fertilization; and sperm-egg recognition. Predicted to be located in extracellular region and plasma membrane. Predicted to be anchored component of external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IZUMO1R | NM_001199206.4 | c.425A>C | p.Asp142Ala | missense_variant | 4/5 | ENST00000687084.1 | |
IZUMO1R | NM_001393610.1 | c.425A>C | p.Asp142Ala | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IZUMO1R | ENST00000687084.1 | c.425A>C | p.Asp142Ala | missense_variant | 4/5 | NM_001199206.4 | |||
IZUMO1R | ENST00000328458.6 | c.425A>C | p.Asp142Ala | missense_variant | 3/4 | 5 | |||
IZUMO1R | ENST00000440961.6 | c.404A>C | p.Asp135Ala | missense_variant | 3/4 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152158Hom.: 0 Cov.: 32
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GnomAD4 exome Cov.: 32
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D
PrimateAI
Benign
T
Polyphen
0.28
.;B
Vest4
0.57
MVP
0.49
MPC
0.061
ClinPred
D
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at