15-40654975-A-G

Position:

• chr15-40654975-A-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BS1_Supporting

The ENST00000399668.7(KNL1):​c.6482A>G​(p.Asp2161Gly) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000187 in 1,611,174 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00092 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00011 (1 hom.)
• Consequence: KNL1 ENST00000399668.7 missense, splice_region
• Scores: Splicing: ADA: 0.4211
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:5 B:1
• Conservation: PhyloP100: 5.34

Genes affected

KNL1 (HGNC:24054): (kinetochore scaffold 1) The protein encoded by this gene is a component of the multiprotein assembly that is required for creation of kinetochore-microtubule attachments and chromosome segregation. The encoded protein functions as a scaffold for proteins that influence the spindle assembly checkpoint during the eukaryotic cell cycle and it interacts with at least five different kinetochore proteins and two checkpoint kinases. In adults, this gene is predominantly expressed in normal testes, various cancer cell lines and primary tumors from other tissues and is ubiquitously expressed in fetal tissues. This gene was originally identified as a fusion partner with the mixed-lineage leukemia (MLL) gene in t(11;15)(q23;q14). Mutations in this gene cause autosomal recessive primary microcephaly-4 (MCPH4). Alternative splicing results in multiple transcript variants encoding different isoforms. Additional splice variants have been described but their biological validity has not been confirmed. [provided by RefSeq, Jan 2013]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.03363198).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00092 (140/152226) while in subpopulation AFR AF= 0.00325 (135/41538). AF 95% confidence interval is 0.0028. There are 1 homozygotes in gnomad4. There are 69 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KNL1	NM_144508.5	c.6482A>G	p.Asp2161Gly	missense_variant, splice_region_variant	22/26	ENST00000399668.7	NP_653091.3
KNL1	NM_170589.5	c.6560A>G	p.Asp2187Gly	missense_variant, splice_region_variant	23/27		NP_733468.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KNL1	ENST00000399668.7	c.6482A>G	p.Asp2161Gly	missense_variant, splice_region_variant	22/26	1	NM_144508.5	ENSP00000382576	A2
KNL1	ENST00000346991.9	c.6560A>G	p.Asp2187Gly	missense_variant, splice_region_variant	23/27	1		ENSP00000335463	P4
KNL1	ENST00000526913.5	c.3617A>G	p.Asp1206Gly	missense_variant, splice_region_variant, NMD_transcript_variant	13/18	1		ENSP00000432565
KNL1	ENST00000532347.1	n.562A>G		non_coding_transcript_exon_variant	5/5	4

Frequencies

GnomAD3 genomes AF: 0.000914 AC: 139 AN: 152108 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00324

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000957

GnomAD3 exomes AF: 0.000261 AC: 65 AN: 248892 Hom.: 0 AF XY: 0.000229 AC XY: 31 AN XY: 135106

Gnomad AFR exome AF: 0.00356

Gnomad AMR exome AF: 0.000203

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000177

Gnomad OTH exome AF: 0.000165

GnomAD4 exome AF: 0.000110 AC: 161 AN: 1458948 Hom.: 1 Cov.: 29 AF XY: 0.0000868 AC XY: 63 AN XY: 726048

Gnomad4 AFR exome AF: 0.00350

Gnomad4 AMR exome AF: 0.000246

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000126

Gnomad4 OTH exome AF: 0.000298

GnomAD4 genome AF: 0.000920 AC: 140 AN: 152226 Hom.: 1 Cov.: 32 AF XY: 0.000927 AC XY: 69 AN XY: 74436

Gnomad4 AFR AF: 0.00325

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.000947

Alfa AF: 0.0000727 Hom.: 0

Bravo AF: 0.00102

ESP6500AA AF: 0.00219 AC: 8

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000298 AC: 36

EpiCase AF: 0.0000546

EpiControl AF: 0.00

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:5 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Microcephaly 4, primary, autosomal recessive Pathogenic:1 Uncertain:3

Pathogenic, no assertion criteria provided	literature only	OMIM	Feb 19, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Daryl Scott Lab, Baylor College of Medicine	Feb 01, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Molecular Genetics Pathology Laboratory, University Of Arkansas for Medical Sciences	Oct 26, 2015	The c. 6560A>G is classified as of unknown significance. Per ACMG criteria, it does have silico prediction criteria PP3. The variant is predicted pathogenic by SIFT, Mutation tasting, Provean (-3.624), and PolyPhen-2 (0.999). The physiochemical difference between Aspartic acid and Glycine is moderate (Grantham score=94) and amino acid analysis conservation by Alamut indicates that the wild type amino acid is moderately conserved. The c.6560A>G variant is very rare in the general population, but particularly found in patients of African ancestry with a reported heterozygous median allele frequency of 0.0034 (33/9694 alleles) in the Exome Aggregation Consortium and 0.0022 (8/3660) in the Exome Variant Server for people of this ancestry. -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 24, 2019	This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -

not provided Uncertain:1 Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Nov 07, 2024	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 28901661, 22983954, 27149178, 36474027) -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jun 26, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Benign	-0.44	T
BayesDel_noAF	Benign	-0.40
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.32	T;.
Eigen	Uncertain	0.56
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.78	T;T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.034	T;T
MetaSVM	Benign	-1.2	T
MutationTaster	Benign	1.0	D;D
PrimateAI	Benign	0.43	T
PROVEAN	Uncertain	-3.6	D;D
REVEL	Benign	0.24
Sift	Uncertain	0.023	D;D
Sift4G	Benign	0.071	T;T
Polyphen		1.0	D;D
Vest4		0.81
MVP		0.71
MPC		0.075
ClinPred		0.091	T
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.66
gMVP		0.37

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.42
dbscSNV1_RF	Benign	0.43
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs142872154; hg19: chr15-40947173;