7-139483485-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198508.4(KLRG2):c.158C>T(p.Ala53Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,596,308 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_198508.4 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 |
---|---|---|---|---|---|---|---|
KLRG2 | NM_198508.4 | c.158C>T | p.Ala53Val | missense_variant | 1/5 | ENST00000340940.5 | |
KLRG2 | XM_011516140.3 | c.158C>T | p.Ala53Val | missense_variant | 1/4 | ||
KLRG2 | XM_011516141.3 | c.158C>T | p.Ala53Val | missense_variant | 1/4 | ||
KLRG2 | XM_005250311.4 | c.158C>T | p.Ala53Val | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLRG2 | ENST00000340940.5 | c.158C>T | p.Ala53Val | missense_variant | 1/5 | 1 | NM_198508.4 | P1 | |
KLRG2 | ENST00000393039.2 | c.158C>T | p.Ala53Val | missense_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000136 AC: 3AN: 220122Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 122748
GnomAD4 exome AF: 0.00000277 AC: 4AN: 1444000Hom.: 0 Cov.: 34 AF XY: 0.00000278 AC XY: 2AN XY: 718816
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 21, 2021 | The c.158C>T (p.A53V) alteration is located in exon 1 (coding exon 1) of the KLRG2 gene. This alteration results from a C to T substitution at nucleotide position 158, causing the alanine (A) at amino acid position 53 to be replaced by a valine (V). 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