dbSNP rs1131863: NCALD:c.*1242A>G (chr8-101688067-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032041.3(NCALD):c.*1242A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,212 control chromosomes in the GnomAD database, including 4,292 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 0.23 ( 4283 hom., cov: 32)

Exomes 𝑓: 0.28 ( 9 hom. )

Consequence

NCALD
NM_032041.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0100

Publications

9 publications found

Variant links:

Genes affected

NCALD (HGNC:7655): (neurocalcin delta) This gene encodes a member of the neuronal calcium sensor (NCS) family of calcium-binding proteins. The protein contains an N-terminal myristoylation signal and four EF-hand calcium binding loops. The protein is cytosolic at resting calcium levels; however, elevated intracellular calcium levels induce a conformational change that exposes the myristoyl group, resulting in protein association with membranes and partial co-localization with the perinuclear trans-golgi network. The protein is thought to be a regulator of G protein-coupled receptor signal transduction. Several alternatively spliced variants of this gene have been determined, all of which encode the same protein; additional variants may exist but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

NCALD links:

ENSG00000253629 (HGNC:):

ENSG00000253629 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCALD	NM_032041.3 link	c.*1242A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000220931.11	NP_114430.2	P61601B2RB70

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCALD	ENST00000220931.11 link	c.*1242A>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_032041.3	ENSP00000220931.6		P61601

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34329

AN:

151974

Hom.:

4292

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.256

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.229

Gnomad MID

AF:

0.338

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.236

GnomAD4 exome

AF:

0.283

AC:

AN:

120

Hom.:

Cov.:

AF XY:

0.278

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.286

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.277

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.226

AC:

34308

AN:

152092

Hom.:

4283

Cov.:

AF XY:

0.227

AC XY:

16907

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.123

AC:

5110

AN:

41496

American (AMR)

AF:

0.302

AC:

4619

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

956

AN:

3466

East Asian (EAS)

AF:

0.255

AC:

1320

AN:

5172

South Asian (SAS)

AF:

0.307

AC:

1477

AN:

4816

European-Finnish (FIN)

AF:

0.229

AC:

2425

AN:

10572

Middle Eastern (MID)

AF:

0.329

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.260

AC:

17704

AN:

67976

Other (OTH)

AF:

0.233

AC:

491

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1340

2680

4021

5361

6701

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.243

Hom.:

6733

Bravo

AF:

0.226

Asia WGS

AF:

0.267

AC:

928

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.6

(source)

DANN

Benign

0.65

PhyloP100

0.010

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs1131863

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over