rs2079867

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014865.4(NCAPD2):​c.588-1320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,056 control chromosomes in the GnomAD database, including 46,716 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 0.78 ( 46716 hom., cov: 31)

Consequence

NCAPD2
NM_014865.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.175
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NCAPD2NM_014865.4 linkuse as main transcriptc.588-1320A>G intron_variant ENST00000315579.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NCAPD2ENST00000315579.10 linkuse as main transcriptc.588-1320A>G intron_variant 1 NM_014865.4 P1
NCAPD2ENST00000382457.8 linkuse as main transcriptc.204-1320A>G intron_variant 5
NCAPD2ENST00000539084.5 linkuse as main transcriptc.*283-1320A>G intron_variant, NMD_transcript_variant 2
NCAPD2ENST00000545732.1 linkuse as main transcriptn.29-1320A>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.780
AC:
118440
AN:
151936
Hom.:
46664
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.905
Gnomad AMI
AF:
0.640
Gnomad AMR
AF:
0.796
Gnomad ASJ
AF:
0.721
Gnomad EAS
AF:
0.669
Gnomad SAS
AF:
0.683
Gnomad FIN
AF:
0.766
Gnomad MID
AF:
0.699
Gnomad NFE
AF:
0.723
Gnomad OTH
AF:
0.757
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.780
AC:
118554
AN:
152056
Hom.:
46716
Cov.:
31
AF XY:
0.780
AC XY:
57925
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.905
Gnomad4 AMR
AF:
0.797
Gnomad4 ASJ
AF:
0.721
Gnomad4 EAS
AF:
0.669
Gnomad4 SAS
AF:
0.683
Gnomad4 FIN
AF:
0.766
Gnomad4 NFE
AF:
0.723
Gnomad4 OTH
AF:
0.756
Alfa
AF:
0.735
Hom.:
44391
Bravo
AF:
0.791
Asia WGS
AF:
0.766
AC:
2662
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
9.5
DANN
Benign
0.80

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs2079867; hg19: chr12-6622111; API