chr3-186731583-T-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001102416.3(KNG1):c.711T>G(p.Ile237Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001102416.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KNG1 | NM_001102416.3 | c.711T>G | p.Ile237Met | missense_variant | 6/10 | ENST00000644859.2 | |
KNG1 | NM_000893.4 | c.711T>G | p.Ile237Met | missense_variant | 6/11 | ||
KNG1 | NM_001166451.2 | c.603T>G | p.Ile201Met | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KNG1 | ENST00000644859.2 | c.711T>G | p.Ile237Met | missense_variant | 6/10 | NM_001102416.3 | |||
HRG-AS1 | ENST00000630178.2 | n.135+12120A>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251308Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135852
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1459970Hom.: 0 Cov.: 28 AF XY: 0.0000262 AC XY: 19AN XY: 726460
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 09, 2022 | The c.711T>G (p.I237M) alteration is located in exon 6 (coding exon 6) of the KNG1 gene. This alteration results from a T to G substitution at nucleotide position 711, causing the isoleucine (I) at amino acid position 237 to be replaced by a methionine (M). 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