rs740850

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_014865.4(NCAPD2):​c.3483C>G​(p.Asn1161Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

NCAPD2
NM_014865.4 missense

Scores

4
7
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19
Variant links:
Genes affected
NCAPD2 (HGNC:24305): (non-SMC condensin I complex subunit D2) Enables histone binding activity. Involved in mitotic chromosome condensation. Located in condensed chromosome; cytosol; and nucleoplasm. Part of condensin complex. Colocalizes with cytoplasm and nuclear chromosome. Implicated in primary autosomal recessive microcephaly. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NCAPD2NM_014865.4 linkuse as main transcriptc.3483C>G p.Asn1161Lys missense_variant 27/32 ENST00000315579.10 NP_055680.3 Q15021B3KY03B3KMS0

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NCAPD2ENST00000315579.10 linkuse as main transcriptc.3483C>G p.Asn1161Lys missense_variant 27/321 NM_014865.4 ENSP00000325017.5 Q15021
NCAPD2ENST00000535804.1 linkuse as main transcriptn.316C>G non_coding_transcript_exon_variant 2/23
NCAPD2ENST00000539084.5 linkuse as main transcriptn.*3178C>G non_coding_transcript_exon_variant 26/312 ENSP00000438495.1 F5H431
NCAPD2ENST00000539084.5 linkuse as main transcriptn.*3178C>G 3_prime_UTR_variant 26/312 ENSP00000438495.1 F5H431

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
39
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.97
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
14
DANN
Uncertain
1.0
DEOGEN2
Benign
0.21
T
Eigen
Benign
-0.099
Eigen_PC
Benign
-0.37
FATHMM_MKL
Benign
0.40
N
LIST_S2
Uncertain
0.90
D
M_CAP
Uncertain
0.098
D
MetaRNN
Uncertain
0.74
D
MetaSVM
Benign
-0.86
T
MutationAssessor
Uncertain
2.5
M
PrimateAI
Uncertain
0.65
T
PROVEAN
Pathogenic
-5.4
D
REVEL
Uncertain
0.37
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.89
MutPred
0.59
Gain of catalytic residue at I1163 (P = 0.0031);
MVP
0.30
MPC
0.80
ClinPred
1.0
D
GERP RS
-4.3
Varity_R
0.95
gMVP
0.67

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

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

Other links and lift over

dbSNP: rs740850; hg19: chr12-6638116; API