chr20-44619661-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000022.4(ADA):c.*173G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00338 in 801,538 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000022.4 3_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 |
---|---|---|---|---|---|---|---|---|
ADA | NM_000022.4 | c.*173G>C | 3_prime_UTR_variant | Exon 12 of 12 | ENST00000372874.9 | NP_000013.2 | ||
ADA | NM_001322051.2 | c.*173G>C | 3_prime_UTR_variant | Exon 11 of 11 | NP_001308980.1 | |||
ADA | NM_001322050.2 | c.*173G>C | 3_prime_UTR_variant | Exon 11 of 11 | NP_001308979.1 | |||
ADA | NR_136160.2 | n.1292G>C | non_coding_transcript_exon_variant | Exon 11 of 11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADA | ENST00000372874 | c.*173G>C | 3_prime_UTR_variant | Exon 12 of 12 | 1 | NM_000022.4 | ENSP00000361965.4 | |||
ADA | ENST00000695995 | c.*173G>C | 3_prime_UTR_variant | Exon 9 of 9 | ENSP00000512318.1 | |||||
ADA | ENST00000695991 | c.*173G>C | 3_prime_UTR_variant | Exon 8 of 8 | ENSP00000512314.1 | |||||
ADA | ENST00000695956 | c.*57G>C | 3_prime_UTR_variant | Exon 3 of 3 | ENSP00000512285.1 | |||||
ADA | ENST00000696038.1 | n.*1473G>C | non_coding_transcript_exon_variant | Exon 9 of 9 | ENSP00000512344.1 | |||||
ADA | ENST00000696038.1 | n.*1473G>C | 3_prime_UTR_variant | Exon 9 of 9 | ENSP00000512344.1 |
Frequencies
GnomAD3 genomes AF: 0.0118 AC: 1794AN: 152174Hom.: 50 Cov.: 33
GnomAD4 exome AF: 0.00142 AC: 919AN: 649246Hom.: 16 Cov.: 9 AF XY: 0.00116 AC XY: 393AN XY: 338980
GnomAD4 genome AF: 0.0118 AC: 1794AN: 152292Hom.: 50 Cov.: 33 AF XY: 0.0112 AC XY: 831AN XY: 74458
ClinVar
Submissions by phenotype
Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency Benign:1
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
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at