Variant chr12-6495252-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014865.4(NCAPD2):c.127+27C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,611,426 control chromosomes in the GnomAD database, including 69,866 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 9273 hom., cov: 32)

Exomes 𝑓: 0.28 ( 60593 hom. )

Consequence

NCAPD2
NM_014865.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.165

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]

NCAPD2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 12-6495252-C-T is Benign according to our data. Variant chr12-6495252-C-T is described in ClinVar as [Benign]. Clinvar id is 1321843.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCAPD2	NM_014865.4 linkuse as main transcript	c.127+27C>T		intron_variant		ENST00000315579.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCAPD2	ENST00000315579.10 linkuse as main transcript	c.127+27C>T		intron_variant		1	NM_014865.4	P1

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51424

AN:

152006

Hom.:

9260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.427

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.368

GnomAD3 exomes

AF:

0.309

AC:

77116

AN:

249948

Hom.:

12657

AF XY:

0.301

AC XY:

40666

AN XY:

135072

show subpopulations

Gnomad AFR exome

AF:

0.471

Gnomad AMR exome

AF:

0.413

Gnomad ASJ exome

AF:

0.421

Gnomad EAS exome

AF:

0.224

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.257

Gnomad NFE exome

AF:

0.289

Gnomad OTH exome

AF:

0.321

GnomAD4 exome

AF:

0.283

AC:

413576

AN:

1459302

Hom.:

60593

Cov.:

AF XY:

0.282

AC XY:

204749

AN XY:

725918

show subpopulations

Gnomad4 AFR exome

AF:

0.477

Gnomad4 AMR exome

AF:

0.409

Gnomad4 ASJ exome

AF:

0.425

Gnomad4 EAS exome

AF:

0.212

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.262

Gnomad4 NFE exome

AF:

0.275

Gnomad4 OTH exome

AF:

0.303

GnomAD4 genome

AF:

0.338

AC:

51475

AN:

152124

Hom.:

9273

Cov.:

AF XY:

0.336

AC XY:

25008

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.360

Gnomad4 ASJ

AF:

0.427

Gnomad4 EAS

AF:

0.221

Gnomad4 SAS

AF:

0.229

Gnomad4 FIN

AF:

0.261

Gnomad4 NFE

AF:

0.282

Gnomad4 OTH

AF:

0.364

Alfa

AF:

0.332

Hom.:

1684

Bravo

AF:

0.357

Asia WGS

AF:

0.261

AC:

910

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Microcephaly 21, primary, autosomal recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.8

DANN

Benign

0.52

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over