dbSNP rs1043262: NCAPD2:p.Val1267Val (chr12-6529922-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014865.4(NCAPD2):c.3801A>G(p.Val1267Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 1,613,992 control chromosomes in the GnomAD database, including 428,983 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.77 ( 45947 hom., cov: 34)

Exomes 𝑓: 0.72 ( 383036 hom. )

Consequence

NCAPD2
NM_014865.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.700

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 12-6529922-A-G is Benign according to our data. Variant chr12-6529922-A-G is described in ClinVar as [Benign]. Clinvar id is 1321849.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.7 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCAPD2	NM_014865.4 link	c.3801A>G	p.Val1267Val	synonymous_variant	Exon 29 of 32	ENST00000315579.10	NP_055680.3	Q15021B3KY03B3KMS0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
NCAPD2	ENST00000315579.10 link	c.3801A>G	p.Val1267Val	synonymous_variant	Exon 29 of 32	1	NM_014865.4	ENSP00000325017.5	Q15021
NCAPD2	ENST00000539084.5 link	n.*3496A>G		non_coding_transcript_exon_variant	Exon 28 of 31	2		ENSP00000438495.1	F5H431
NCAPD2	ENST00000539885.1 link	n.482A>G		non_coding_transcript_exon_variant	Exon 2 of 3	3
NCAPD2	ENST00000539084.5 link	n.*3496A>G		3_prime_UTR_variant	Exon 28 of 31	2		ENSP00000438495.1	F5H431

Frequencies

GnomAD3 genomes

AF:

0.772

AC:

117493

AN:

152098

Hom.:

45896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.898

Gnomad AMI

AF:

0.613

Gnomad AMR

AF:

0.790

Gnomad ASJ

AF:

0.713

Gnomad EAS

AF:

0.696

Gnomad SAS

AF:

0.674

Gnomad FIN

AF:

0.756

Gnomad MID

AF:

0.693

Gnomad NFE

AF:

0.714

Gnomad OTH

AF:

0.749

GnomAD3 exomes

AF:

0.744

AC:

186921

AN:

251378

Hom.:

70100

AF XY:

0.733

AC XY:

99623

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.901

Gnomad AMR exome

AF:

0.860

Gnomad ASJ exome

AF:

0.703

Gnomad EAS exome

AF:

0.693

Gnomad SAS exome

AF:

0.691

Gnomad FIN exome

AF:

0.753

Gnomad NFE exome

AF:

0.711

Gnomad OTH exome

AF:

0.730

GnomAD4 exome

AF:

0.723

AC:

1056491

AN:

1461776

Hom.:

383036

Cov.:

AF XY:

0.720

AC XY:

523942

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.907

Gnomad4 AMR exome

AF:

0.854

Gnomad4 ASJ exome

AF:

0.708

Gnomad4 EAS exome

AF:

0.686

Gnomad4 SAS exome

AF:

0.683

Gnomad4 FIN exome

AF:

0.754

Gnomad4 NFE exome

AF:

0.715

Gnomad4 OTH exome

AF:

0.727

GnomAD4 genome

AF:

0.773

AC:

117606

AN:

152216

Hom.:

45947

Cov.:

AF XY:

0.772

AC XY:

57471

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.898

Gnomad4 AMR

AF:

0.791

Gnomad4 ASJ

AF:

0.713

Gnomad4 EAS

AF:

0.697

Gnomad4 SAS

AF:

0.674

Gnomad4 FIN

AF:

0.756

Gnomad4 NFE

AF:

0.713

Gnomad4 OTH

AF:

0.749

Alfa

AF:

0.727

Hom.:

19205

Bravo

AF:

0.784

Asia WGS

AF:

0.766

AC:

2665

AN:

3478

EpiCase

AF:

0.705

EpiControl

AF:

0.691

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Microcephaly 21, primary, autosomal recessive

Benign:1

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.0

DANN

Benign

0.64

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