20-16367512-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000408042.5(KIF16B):āc.3813C>Gā(p.Asn1271Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000598 in 1,612,882 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
ENST00000408042.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF16B | NM_024704.5 | c.3498+3074C>G | intron_variant | ENST00000354981.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF16B | ENST00000408042.5 | c.3813C>G | p.Asn1271Lys | missense_variant | 23/23 | 1 | |||
KIF16B | ENST00000354981.7 | c.3498+3074C>G | intron_variant | 1 | NM_024704.5 | P1 | |||
KIF16B | ENST00000636835.1 | c.3345+3074C>G | intron_variant | 1 | |||||
KIF16B | ENST00000635823.2 | c.5133C>G | p.Asn1711Lys | missense_variant | 23/23 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00110 AC: 265AN: 241516Hom.: 3 AF XY: 0.00146 AC XY: 194AN XY: 132616
GnomAD4 exome AF: 0.000624 AC: 912AN: 1460546Hom.: 8 Cov.: 32 AF XY: 0.000917 AC XY: 666AN XY: 726568
GnomAD4 genome AF: 0.000341 AC: 52AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.000362 AC XY: 27AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | KIF16B: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at