ENST00000521599.5:c.-210+43372T>C

Variant names:

• chr8-102080865-A-G
• rs7830150
• ENST00000521599.5:c.-210+43372T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521599.5(NCALD):​c.-210+43372T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,224 control chromosomes in the GnomAD database, including 2,908 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 0.18 (2908 hom., cov: 32)
• Consequence: NCALD ENST00000521599.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961
• Publications: 6 publications found

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]

ENSG00000310398 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521599.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCALD	NM_001040624.2		c.-297+43372T>C		intron	N/A	NP_001035714.1	P61601
	NCALD	NM_001040625.2		c.-210+43372T>C		intron	N/A	NP_001035715.1	P61601
	NCALD	NM_001040626.2		c.-210+43372T>C		intron	N/A	NP_001035716.1	B2RB70

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCALD	ENST00000521599.5	TSL:1	c.-210+43372T>C		intron	N/A	ENSP00000428105.1	P61601
	NCALD	ENST00000311028.4	TSL:5	c.-210+43372T>C		intron	N/A	ENSP00000310587.3	P61601
	NCALD	ENST00000395923.5	TSL:5	c.-123+43705T>C		intron	N/A	ENSP00000379256.1	P61601

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27070 AN: 152104 Hom.: 2908 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.178 AC: 27079 AN: 152224 Hom.: 2908 Cov.: 32 AF XY: 0.174 AC XY: 12961 AN XY: 74442

African (AFR) AF: 0.297 AC: 12329 AN: 41490

American (AMR) AF: 0.144 AC: 2208 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3470

East Asian (EAS) AF: 0.128 AC: 662 AN: 5182

South Asian (SAS) AF: 0.162 AC: 781 AN: 4826

European-Finnish (FIN) AF: 0.121 AC: 1288 AN: 10624

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8983 AN: 68020

Other (OTH) AF: 0.153 AC: 322 AN: 2110

Alfa AF: 0.142 Hom.: 7357

Bravo AF: 0.182

Asia WGS AF: 0.171 AC: 592 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	0.28
DANN	Benign	0.54
PhyloP100		-0.96
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7830150;

hg19: chr8-103093093;