rs1125334

chr8-101742646-C-Achr8-101742646-C-Gchr8-101742646-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032041.3(NCALD):c.-19-22998G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,960 control chromosomes in the GnomAD database, including 30,977 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 0.61 (30977 hom., cov: 32)
• Consequence: NCALD NM_032041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCALD	NM_032041.3	c.-19-22998G>T		intron_variant		ENST00000220931.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCALD	ENST00000220931.11	c.-19-22998G>T		intron_variant		1	NM_032041.3	P1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92550 AN: 151842 Hom.: 30981 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.609 AC: 92548 AN: 151960 Hom.: 30977 Cov.: 32 AF XY: 0.614 AC XY: 45611 AN XY: 74302

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.644

Alfa AF: 0.722 Hom.: 29777

Bravo AF: 0.574

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.7
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

Other links and lift over

dbSNP: rs1125334; hg19: chr8-102754874;