rs13381300

Variant names:

• chr18-2572096-T-G
• rs13381300
• NM_006101.3:c.-10+413T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006101.3(NDC80):​c.-10+413T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0946 in 152,164 control chromosomes in the GnomAD database, including 949 homozygotes. 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: 𝑓 0.095 (949 hom., cov: 33)
• Consequence: NDC80 NM_006101.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 5 publications found

Genes affected

NDC80 (HGNC:16909): (NDC80 kinetochore complex component) This gene encodes a component of the NDC80 kinetochore complex. The encoded protein consists of an N-terminal microtubule binding domain and a C-terminal coiled-coiled domain that interacts with other components of the complex. This protein functions to organize and stabilize microtubule-kinetochore interactions and is required for proper chromosome segregation. [provided by RefSeq, Oct 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006101.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDC80	NM_006101.3	MANE Select	c.-10+413T>G		intron	N/A	NP_006092.1	O14777

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDC80	ENST00000261597.9	TSL:1 MANE Select	c.-10+413T>G		intron	N/A	ENSP00000261597.4	O14777
	NDC80	ENST00000887758.1		c.-890T>G		5_prime_UTR	Exon 1 of 16	ENSP00000557817.1
	NDC80	ENST00000929147.1		c.-10+413T>G		intron	N/A	ENSP00000599206.1

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14377 AN: 152046 Hom.: 947 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0963

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0946 AC: 14394 AN: 152164 Hom.: 949 Cov.: 33 AF XY: 0.0908 AC XY: 6757 AN XY: 74382

African (AFR) AF: 0.190 AC: 7866 AN: 41498

American (AMR) AF: 0.0659 AC: 1008 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4822

European-Finnish (FIN) AF: 0.0202 AC: 214 AN: 10590

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0667 AC: 4536 AN: 67994

Other (OTH) AF: 0.0962 AC: 203 AN: 2110

Alfa AF: 0.0725 Hom.: 689

Bravo AF: 0.101

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.35
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13381300; hg19: chr18-2572095;