17-5020048-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_006612.6(KIF1C):c.1719G>A(p.Lys573Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,450,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006612.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF1C | NM_006612.6 | c.1719G>A | p.Lys573Lys | synonymous_variant | Exon 19 of 23 | ENST00000320785.10 | NP_006603.2 | |
KIF1C | XM_005256424.3 | c.1719G>A | p.Lys573Lys | synonymous_variant | Exon 20 of 24 | XP_005256481.1 | ||
KIF1C-AS1 | NR_120665.2 | n.46C>T | non_coding_transcript_exon_variant | Exon 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF1C | ENST00000320785.10 | c.1719G>A | p.Lys573Lys | synonymous_variant | Exon 19 of 23 | 1 | NM_006612.6 | ENSP00000320821.5 | ||
KIF1C-AS1 | ENST00000438266.1 | n.46C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
KIF1C | ENST00000573815.1 | n.261G>A | non_coding_transcript_exon_variant | Exon 3 of 6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1450572Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 720364
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
KIF1C: PM2:Supporting, BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.