chr11-134152936-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1

The NM_015261.3(NCAPD3):​c.*8C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000711 in 1,532,560 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000043 ( 0 hom. )

Consequence

NCAPD3
NM_015261.3 3_prime_UTR

Scores

2

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.202
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 11-134152936-G-A is Benign according to our data. Variant chr11-134152936-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3354212.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000328 (50/152318) while in subpopulation AFR AF= 0.00106 (44/41572). AF 95% confidence interval is 0.000809. There are 0 homozygotes in gnomad4. There are 27 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NCAPD3NM_015261.3 linkc.*8C>T 3_prime_UTR_variant Exon 35 of 35 ENST00000534548.7 NP_056076.1 P42695

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NCAPD3ENST00000534548 linkc.*8C>T 3_prime_UTR_variant Exon 35 of 35 1 NM_015261.3 ENSP00000433681.3 P42695

Frequencies

GnomAD3 genomes
AF:
0.000322
AC:
49
AN:
152200
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00104
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000126
AC:
24
AN:
191190
Hom.:
0
AF XY:
0.0000994
AC XY:
10
AN XY:
100570
show subpopulations
Gnomad AFR exome
AF:
0.00122
Gnomad AMR exome
AF:
0.0000811
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000607
Gnomad SAS exome
AF:
0.0000616
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000110
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000427
AC:
59
AN:
1380242
Hom.:
0
Cov.:
30
AF XY:
0.0000354
AC XY:
24
AN XY:
677986
show subpopulations
Gnomad4 AFR exome
AF:
0.00127
Gnomad4 AMR exome
AF:
0.0000900
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000256
Gnomad4 SAS exome
AF:
0.0000416
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000560
Gnomad4 OTH exome
AF:
0.000123
GnomAD4 genome
AF:
0.000328
AC:
50
AN:
152318
Hom.:
0
Cov.:
33
AF XY:
0.000363
AC XY:
27
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.00106
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000427
Hom.:
0
Bravo
AF:
0.000321
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

NCAPD3-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 20, 2024This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.72
DANN
Benign
0.65

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200642279; hg19: chr11-134022831; API