7-140673700-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052853.4(ADCK2):c.370C>T(p.Pro124Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000698 in 1,612,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052853.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADCK2 | NM_052853.4 | c.370C>T | p.Pro124Ser | missense_variant | Exon 1 of 8 | ENST00000072869.9 | NP_443085.2 | |
ADCK2 | XM_011516675.4 | c.370C>T | p.Pro124Ser | missense_variant | Exon 1 of 7 | XP_011514977.1 | ||
ADCK2 | XM_006716170.5 | c.370C>T | p.Pro124Ser | missense_variant | Exon 1 of 7 | XP_006716233.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADCK2 | ENST00000072869.9 | c.370C>T | p.Pro124Ser | missense_variant | Exon 1 of 8 | 1 | NM_052853.4 | ENSP00000072869.4 | ||
ADCK2 | ENST00000476491.5 | c.370C>T | p.Pro124Ser | missense_variant | Exon 1 of 8 | 1 | ENSP00000420512.1 | |||
DENND2A | ENST00000489552.1 | c.-146+174G>A | intron_variant | Intron 1 of 1 | 4 | ENSP00000418088.1 | ||||
ADCK2 | ENST00000483369.5 | c.-120C>T | upstream_gene_variant | 5 | ENSP00000417367.1 |
Frequencies
GnomAD3 genomes AF: 0.000612 AC: 93AN: 152048Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000364 AC: 91AN: 250048Hom.: 0 AF XY: 0.000385 AC XY: 52AN XY: 135206
GnomAD4 exome AF: 0.000708 AC: 1033AN: 1460012Hom.: 0 Cov.: 32 AF XY: 0.000647 AC XY: 470AN XY: 726352
GnomAD4 genome AF: 0.000611 AC: 93AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.370C>T (p.P124S) alteration is located in exon 1 (coding exon 1) of the ADCK2 gene. This alteration results from a C to T substitution at nucleotide position 370, causing the proline (P) at amino acid position 124 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at