rs3092980

Variant names:

• chr15-40651905-C-G
• rs3092980
• NM_144508.5:c.6315-100C>G

Your query was ambiguous. Multiple possible variants found:

• chr15-40651905-C-G
• chr15-40651905-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_144508.5(KNL1):​c.6315-100C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000189 in 529,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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: 0.0000019 (0 hom.)
• Consequence: KNL1 NM_144508.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 3 publications found

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]

KNL1 Gene-Disease associations (from GenCC):

• microcephaly 4, primary, autosomal recessive

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• autosomal recessive primary microcephaly

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KNL1	NM_144508.5	c.6315-100C>G		intron_variant	Intron 20 of 25	ENST00000399668.7	NP_653091.3
KNL1	NM_170589.5	c.6393-100C>G		intron_variant	Intron 21 of 26		NP_733468.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KNL1	ENST00000399668.7	c.6315-100C>G		intron_variant	Intron 20 of 25	1	NM_144508.5	ENSP00000382576.3
KNL1	ENST00000346991.9	c.6393-100C>G		intron_variant	Intron 21 of 26	1		ENSP00000335463.6
KNL1	ENST00000526913.5	n.3447-100C>G		intron_variant	Intron 11 of 17	1		ENSP00000432565.1
KNL1	ENST00000532347.1	n.395-100C>G		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000189 AC: 1 AN: 529048 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 278524

African (AFR) AF: 0.00 AC: 0 AN: 14308

American (AMR) AF: 0.00 AC: 0 AN: 22418

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15944

East Asian (EAS) AF: 0.0000318 AC: 1 AN: 31490

South Asian (SAS) AF: 0.00 AC: 0 AN: 45416

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38826

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3574

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 328690

Other (OTH) AF: 0.00 AC: 0 AN: 28382

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 64

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.69
PhyloP100		-0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3092980; hg19: chr15-40944103;