rs193920855

Variant names:

• chr20-16427128-C-A
• NM_024704.5:c.1588G>T

Your query was ambiguous. Multiple possible variants found:

• chr20-16427128-C-A
• chr20-16427128-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_024704.5(KIF16B):​c.1588G>T​(p.Val530Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,456,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: KIF16B NM_024704.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

Genes affected

KIF16B (HGNC:15869): (kinesin family member 16B) The protein encoded by this gene is a kinesin-like protein that may be involved in intracellular trafficking. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08679718).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF16B	NM_024704.5	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 26	ENST00000354981.7	NP_078980.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF16B	ENST00000354981.7	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 26	1	NM_024704.5	ENSP00000347076.2
KIF16B	ENST00000408042.5	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 23	1		ENSP00000384164.1
KIF16B	ENST00000636835.1	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 25	1		ENSP00000489838.1
KIF16B	ENST00000635823.2	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 23	5		ENSP00000490639.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.87e-7 AC: 1 AN: 1456130 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 724150

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000118

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	2.2
DANN	Benign	0.90
DEOGEN2	Benign	0.14	T;T;.
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.070	N
LIST_S2	Benign	0.68	T;T;T
M_CAP	Benign	0.062	D
MetaRNN	Benign	0.087	T;T;T
MetaSVM	Benign	-0.85	T
MutationAssessor	Benign	0.10	N;.;N
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.71	N;.;N
REVEL	Benign	0.24
Sift	Benign	0.077	T;.;T
Sift4G	Benign	0.30	T;.;T
Polyphen		0.0	B;.;B
Vest4		0.043
MutPred		0.54		Loss of catalytic residue at V530 (P = 0.0338);Loss of catalytic residue at V530 (P = 0.0338);Loss of catalytic residue at V530 (P = 0.0338);
MVP		0.48
MPC		0.11
ClinPred		0.070	T
GERP RS		-4.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.075
gMVP		0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-16407773;