rs1031381

Positions:

• chr11-134218788-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015261.3(NCAPD3):​c.220-1690C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,822 control chromosomes in the GnomAD database, including 10,728 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 0.36 (10728 hom., cov: 32)
• Consequence: NCAPD3 NM_015261.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

NCAPD3 (HGNC:28952): (non-SMC condensin II complex subunit D3) Condensin complexes I and II play essential roles in mitotic chromosome assembly and segregation. Both condensins contain 2 invariant structural maintenance of chromosome (SMC) subunits, SMC2 (MIM 605576) and SMC4 (MIM 605575), but they contain different sets of non-SMC subunits. NCAPD3 is 1 of 3 non-SMC subunits that define condensin II (Ono et al., 2003 [PubMed 14532007]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCAPD3	NM_015261.3	c.220-1690C>T		intron_variant		ENST00000534548.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCAPD3	ENST00000534548.7	c.220-1690C>T		intron_variant		1	NM_015261.3	P2

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55050 AN: 151704 Hom.: 10723 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.363 AC: 55073 AN: 151822 Hom.: 10728 Cov.: 32 AF XY: 0.367 AC XY: 27223 AN XY: 74184

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.392

Alfa AF: 0.400 Hom.: 29258

Bravo AF: 0.365

Asia WGS AF: 0.513 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.42

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

Publications

LitVar

Other links and lift over

dbSNP: rs1031381; hg19: chr11-134088682;