chr7-139480242-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.763C>T(p.Pro255Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,592,140 control chromosomes in the GnomAD database, including 1 homozygotes. 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_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.763C>T | p.Pro255Ser | missense_variant | 2/5 | ENST00000340940.5 | |
KLRG2 | XM_011516140.3 | c.763C>T | p.Pro255Ser | missense_variant | 2/4 | ||
KLRG2 | XM_011516141.3 | c.763C>T | p.Pro255Ser | missense_variant | 2/4 | ||
KLRG2 | XM_005250311.4 | c.763C>T | p.Pro255Ser | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLRG2 | ENST00000340940.5 | c.763C>T | p.Pro255Ser | missense_variant | 2/5 | 1 | NM_198508.4 | P1 | |
KLRG2 | ENST00000393039.2 | c.757+2644C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000725 AC: 11AN: 151824Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000877 AC: 22AN: 250786Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135612
GnomAD4 exome AF: 0.0000389 AC: 56AN: 1440196Hom.: 1 Cov.: 27 AF XY: 0.0000362 AC XY: 26AN XY: 717820
GnomAD4 genome ? AF: 0.0000724 AC: 11AN: 151944Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.763C>T (p.P255S) alteration is located in exon 2 (coding exon 2) of the KLRG2 gene. This alteration results from a C to T substitution at nucleotide position 763, causing the proline (P) at amino acid position 255 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