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GeneBe

rs2155235

Variant summary

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

The ENST00000521599.5(NCALD):c.-209-26303G>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
ENST00000521599.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.600
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]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NCALDNM_001040624.2 linkuse as main transcriptc.-296-26303G>A intron_variant
NCALDNM_001040625.2 linkuse as main transcriptc.-209-26303G>A intron_variant
NCALDNM_001040626.2 linkuse as main transcriptc.-209-35110G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NCALDENST00000521599.5 linkuse as main transcriptc.-209-26303G>A intron_variant 1 P1
NCALDENST00000311028.4 linkuse as main transcriptc.-209-35110G>A intron_variant 5 P1
NCALDENST00000395923.5 linkuse as main transcriptc.-122-35110G>A intron_variant 5 P1

Frequencies

GnomAD3 genomes
AF:
0.111
AC:
16900
AN:
152010
Hom.:
1002
Cov.:
32
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.:
32
AF XY:
0.109
AC XY:
8071
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.113
Gnomad4 AMR
AF:
0.106
Gnomad4 ASJ
AF:
0.171
Gnomad4 EAS
AF:
0.00116
Gnomad4 SAS
AF:
0.0294
Gnomad4 FIN
AF:
0.114
Gnomad4 NFE
AF:
0.121
Gnomad4 OTH
AF:
0.111
Alfa
AF:
0.121
Hom.:
1531
Bravo
AF:
0.113
Asia WGS
AF:
0.0330
AC:
114
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
2.6
Dann
Benign
0.77

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.

Other links and lift over

dbSNP: rs2155235; hg19: chr8-103067627; API