chr12-117476519-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_173598.6(KSR2):c.2527G>A(p.Asp843Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000472 in 1,608,708 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_173598.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000417 AC: 10AN: 239842Hom.: 0 AF XY: 0.0000385 AC XY: 5AN XY: 129786
GnomAD4 exome AF: 0.0000481 AC: 70AN: 1456474Hom.: 0 Cov.: 31 AF XY: 0.0000525 AC XY: 38AN XY: 723830
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74376
ClinVar
Submissions by phenotype
KSR2-related disorder Uncertain:1
The KSR2 c.2440G>A variant is predicted to result in the amino acid substitution p.Asp814Asn. This variant was previously reported in one patient with severe early-onset obesity; however, no additional information was available to help clarify the pathogenicity of this variant (Pearce et al. 2013. PubMed ID: 24209692, reported as D843N). This variant is reported in 0.012% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at