rs199714731
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005148.4(UNC119):c.65G>T(p.Gly22Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,570,244 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005148.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC119 | NM_005148.4 | c.65G>T | p.Gly22Val | missense_variant | 1/5 | ENST00000335765.9 | |
UNC119 | NM_054035.2 | c.65G>T | p.Gly22Val | missense_variant | 1/4 | ||
UNC119 | XM_011525459.3 | c.65G>T | p.Gly22Val | missense_variant | 1/3 | ||
UNC119 | NM_001330166.2 | c.-249G>T | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC119 | ENST00000335765.9 | c.65G>T | p.Gly22Val | missense_variant | 1/5 | 1 | NM_005148.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00632 AC: 962AN: 152142Hom.: 11 Cov.: 31
GnomAD3 exomes AF: 0.00160 AC: 290AN: 181372Hom.: 4 AF XY: 0.00132 AC XY: 135AN XY: 102142
GnomAD4 exome AF: 0.000618 AC: 877AN: 1417996Hom.: 5 Cov.: 31 AF XY: 0.000558 AC XY: 393AN XY: 704522
GnomAD4 genome ? AF: 0.00638 AC: 971AN: 152248Hom.: 12 Cov.: 31 AF XY: 0.00648 AC XY: 482AN XY: 74434
ClinVar
Submissions by phenotype
Idiopathic CD4 lymphocytopenia Pathogenic:1Benign:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 09, 2012 | - - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 28, 2015 | - - |
Cone-rod dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at