chr1-244437682-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001126.5(ADSS2):c.270T>A(p.Asn90Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000817 in 1,590,222 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_001126.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADSS2 | NM_001126.5 | c.270T>A | p.Asn90Lys | missense_variant | 2/13 | ENST00000366535.4 | |
ADSS2 | NM_001365073.2 | c.270T>A | p.Asn90Lys | missense_variant | 2/13 | ||
ADSS2 | XM_047447581.1 | c.90T>A | p.Asn30Lys | missense_variant | 3/14 | ||
ADSS2 | XM_047447585.1 | c.90T>A | p.Asn30Lys | missense_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADSS2 | ENST00000366535.4 | c.270T>A | p.Asn90Lys | missense_variant | 2/13 | 1 | NM_001126.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251296Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135820
GnomAD4 exome AF: 0.00000626 AC: 9AN: 1437896Hom.: 0 Cov.: 29 AF XY: 0.00000837 AC XY: 6AN XY: 716626
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 2023 | The c.270T>A (p.N90K) alteration is located in exon 2 (coding exon 2) of the ADSS gene. This alteration results from a T to A substitution at nucleotide position 270, causing the asparagine (N) at amino acid position 90 to be replaced by a lysine (K). 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