9-100099331-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014425.5(INVS):c.-110T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 153,298 control chromosomes in the GnomAD database, including 3,521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014425.5 5_prime_UTR
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
INVS | NM_014425.5 | c.-110T>G | 5_prime_UTR_variant | Exon 1 of 17 | ENST00000262457.7 | NP_055240.2 | ||
INVS | NM_001318381.2 | c.-486T>G | 5_prime_UTR_variant | Exon 1 of 18 | NP_001305310.1 | |||
INVS | NM_001318382.2 | c.-1099T>G | 5_prime_UTR_variant | Exon 1 of 17 | NP_001305311.1 | |||
INVS | NR_134606.2 | n.89T>G | non_coding_transcript_exon_variant | Exon 1 of 17 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.175 AC: 26656AN: 151948Hom.: 3477 Cov.: 31
GnomAD4 exome AF: 0.262 AC: 323AN: 1232Hom.: 43 Cov.: 0 AF XY: 0.261 AC XY: 221AN XY: 846
GnomAD4 genome AF: 0.175 AC: 26666AN: 152066Hom.: 3478 Cov.: 31 AF XY: 0.184 AC XY: 13655AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:2
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in 1000Genomes: 634/2178=29.1% -
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Kidney disorder Benign:1
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Nephronophthisis Benign:1
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not provided Benign:1
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Infantile nephronophthisis Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at