dbSNP rs2155235: NCALD:c.-209-26303G>A (chr8-102055399-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001040624.2(NCALD):c.-296-26303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,128 control chromosomes in the GnomAD database, including 1,000 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 0.11 ( 1000 hom., cov: 32)

Consequence

NCALD
NM_001040624.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.600

Publications

3 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:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040624.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
NCALD	NM_001040624.2	c.-296-26303G>A	intron	N/A	NP_001035714.1	P61601
NCALD	NM_001040625.2	c.-209-26303G>A	intron	N/A	NP_001035715.1	P61601
NCALD	NM_001040626.2	c.-209-35110G>A	intron	N/A	NP_001035716.1	B2RB70

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NCALD	ENST00000521599.5	TSL:1	c.-209-26303G>A	intron	N/A	ENSP00000428105.1	P61601
NCALD	ENST00000311028.4	TSL:5	c.-209-35110G>A	intron	N/A	ENSP00000310587.3	P61601
NCALD	ENST00000395923.5	TSL:5	c.-122-35110G>A	intron	N/A	ENSP00000379256.1	P61601

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16900

AN:

152010

Hom.:

1002

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0288

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.150

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.113

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.111

AC:

16900

AN:

152128

Hom.:

1000

Cov.:

AF XY:

0.109

AC XY:

8071

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.113

AC:

4677

AN:

41496

American (AMR)

AF:

0.106

AC:

1615

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

593

AN:

3468

East Asian (EAS)

AF:

0.00116

AC:

AN:

5182

South Asian (SAS)

AF:

0.0294

AC:

142

AN:

4824

European-Finnish (FIN)

AF:

0.114

AC:

1204

AN:

10578

Middle Eastern (MID)

AF:

0.147

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.121

AC:

8208

AN:

67982

Other (OTH)

AF:

0.111

AC:

235

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

774

1548

2322

3096

3870

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.121

Hom.:

1928

Bravo

AF:

0.113

Asia WGS

AF:

0.0330

AC:

114

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.6

(source)

DANN

Benign

0.77

PhyloP100

-0.60

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over