rs1656922
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001102416.3(KNG1):c.533T>C(p.Met178Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 1,613,118 control chromosomes in the GnomAD database, including 220,800 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001102416.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KNG1 | NM_001102416.3 | c.533T>C | p.Met178Thr | missense_variant | 4/10 | ENST00000644859.2 | |
KNG1 | NM_000893.4 | c.533T>C | p.Met178Thr | missense_variant | 4/11 | ||
KNG1 | NM_001166451.2 | c.533T>C | p.Met178Thr | missense_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KNG1 | ENST00000644859.2 | c.533T>C | p.Met178Thr | missense_variant | 4/10 | NM_001102416.3 | |||
HRG-AS1 | ENST00000630178.2 | n.136-6660A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.540 AC: 81960AN: 151836Hom.: 22314 Cov.: 31
GnomAD3 exomes AF: 0.537 AC: 135013AN: 251444Hom.: 36947 AF XY: 0.533 AC XY: 72398AN XY: 135900
GnomAD4 exome AF: 0.519 AC: 757954AN: 1461164Hom.: 198468 Cov.: 44 AF XY: 0.519 AC XY: 376984AN XY: 726924
GnomAD4 genome ? AF: 0.540 AC: 82034AN: 151954Hom.: 22332 Cov.: 31 AF XY: 0.539 AC XY: 40039AN XY: 74282
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at