chr19-2098295-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039846.2(IZUMO4):c.482C>T(p.Ala161Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039846.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IZUMO4 | NM_001039846.2 | c.482C>T | p.Ala161Val | missense_variant | Exon 6 of 10 | ENST00000395301.8 | NP_001034935.1 | |
IZUMO4 | NM_001031735.3 | c.482C>T | p.Ala161Val | missense_variant | Exon 6 of 9 | NP_001026905.2 | ||
IZUMO4 | NM_001363588.2 | c.482C>T | p.Ala161Val | missense_variant | Exon 6 of 8 | NP_001350517.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000235 AC: 59AN: 251176Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135806
GnomAD4 exome AF: 0.000168 AC: 246AN: 1461554Hom.: 0 Cov.: 34 AF XY: 0.000173 AC XY: 126AN XY: 727070
GnomAD4 genome AF: 0.000282 AC: 43AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.482C>T (p.A161V) alteration is located in exon 6 (coding exon 6) of the IZUMO4 gene. This alteration results from a C to T substitution at nucleotide position 482, causing the alanine (A) at amino acid position 161 to be replaced by a valine (V). 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