chr1-167818241-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_018417.6(ADCY10):c.4313A>G(p.Asn1438Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0099 in 1,614,074 control chromosomes in the GnomAD database, including 112 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_018417.6 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 |
---|---|---|---|---|---|---|---|
ADCY10 | NM_018417.6 | c.4313A>G | p.Asn1438Ser | missense_variant | 31/33 | ENST00000367851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY10 | ENST00000367851.9 | c.4313A>G | p.Asn1438Ser | missense_variant | 31/33 | 1 | NM_018417.6 | P1 | |
ADCY10 | ENST00000367848.1 | c.4037A>G | p.Asn1346Ser | missense_variant | 31/33 | 1 | |||
ADCY10 | ENST00000545172.5 | c.3854A>G | p.Asn1285Ser | missense_variant | 28/30 | 2 | |||
ADCY10 | ENST00000485964.5 | c.*1249A>G | 3_prime_UTR_variant, NMD_transcript_variant | 13/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00814 AC: 1238AN: 152178Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00814 AC: 2048AN: 251454Hom.: 13 AF XY: 0.00849 AC XY: 1154AN XY: 135900
GnomAD4 exome AF: 0.0101 AC: 14743AN: 1461778Hom.: 107 Cov.: 31 AF XY: 0.0100 AC XY: 7287AN XY: 727192
GnomAD4 genome ? AF: 0.00814 AC: 1239AN: 152296Hom.: 5 Cov.: 33 AF XY: 0.00780 AC XY: 581AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 06, 2023 | See Variant Classification Assertion Criteria. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at