1-167809689-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_018417.6(ADCY10):c.4822A>G(p.Asn1608Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,614,164 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018417.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY10 | NM_018417.6 | c.4822A>G | p.Asn1608Asp | missense_variant | 33/33 | ENST00000367851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY10 | ENST00000367851.9 | c.4822A>G | p.Asn1608Asp | missense_variant | 33/33 | 1 | NM_018417.6 | P1 | |
ADCY10 | ENST00000367848.1 | c.4546A>G | p.Asn1516Asp | missense_variant | 33/33 | 1 | |||
ADCY10 | ENST00000545172.5 | c.4363A>G | p.Asn1455Asp | missense_variant | 30/30 | 2 | |||
ADCY10 | ENST00000485964.5 | c.*1758A>G | 3_prime_UTR_variant, NMD_transcript_variant | 15/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000374 AC: 57AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000143 AC: 36AN: 251438Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135890
GnomAD4 exome AF: 0.0000773 AC: 113AN: 1461798Hom.: 1 Cov.: 31 AF XY: 0.0000660 AC XY: 48AN XY: 727194
GnomAD4 genome AF: 0.000413 AC: 63AN: 152366Hom.: 1 Cov.: 32 AF XY: 0.000429 AC XY: 32AN XY: 74510
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | This sequence change replaces asparagine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 1608 of the ADCY10 protein (p.Asn1608Asp). This variant is present in population databases (rs112911097, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with ADCY10-related conditions. ClinVar contains an entry for this variant (Variation ID: 2076779). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at