chr19-54819970-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_013289.4(KIR3DL1):āc.613C>Gā(p.Gln205Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,611,386 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_013289.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIR3DL1 | NM_013289.4 | c.613C>G | p.Gln205Glu | missense_variant | 4/9 | NP_037421.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIR3DL1 | ENST00000391728.8 | c.613C>G | p.Gln205Glu | missense_variant | 4/9 | 1 | ENSP00000375608.4 | |||
KIR3DL1 | ENST00000326542.11 | c.613C>G | p.Gln205Glu | missense_variant | 4/8 | 1 | ENSP00000326868.7 | |||
KIR3DL1 | ENST00000358178.4 | c.328C>G | p.Gln110Glu | missense_variant | 3/8 | 1 | ENSP00000350901.4 |
Frequencies
GnomAD3 genomes AF: 0.0000396 AC: 6AN: 151448Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000107 AC: 25AN: 233374Hom.: 6 AF XY: 0.000159 AC XY: 20AN XY: 125894
GnomAD4 exome AF: 0.0000295 AC: 43AN: 1459938Hom.: 3 Cov.: 33 AF XY: 0.0000358 AC XY: 26AN XY: 726304
GnomAD4 genome AF: 0.0000396 AC: 6AN: 151448Hom.: 1 Cov.: 33 AF XY: 0.0000541 AC XY: 4AN XY: 73934
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 18, 2021 | The c.613C>G (p.Q205E) alteration is located in exon 4 (coding exon 4) of the KIR3DL1 gene. This alteration results from a C to G substitution at nucleotide position 613, causing the glutamine (Q) at amino acid position 205 to be replaced by a glutamic acid (E). 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