rs16868941

Positions:

• chr8-102040149-G-A

Variant summary

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

The ENST00000521599.5(NCALD):​c.-209-11053C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,116 control chromosomes in the GnomAD database, including 2,500 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 (2500 hom., cov: 32)
• Consequence: NCALD ENST00000521599.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCALD	NM_001040624.2	c.-296-11053C>T		intron_variant
NCALD	NM_001040625.2	c.-209-11053C>T		intron_variant
NCALD	NM_001040626.2	c.-209-19860C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCALD	ENST00000521599.5	c.-209-11053C>T		intron_variant		1		P1
NCALD	ENST00000311028.4	c.-209-19860C>T		intron_variant		5		P1
NCALD	ENST00000395923.5	c.-122-19860C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26798 AN: 151998 Hom.: 2498 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0638

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.176 AC: 26822 AN: 152116 Hom.: 2500 Cov.: 32 AF XY: 0.174 AC XY: 12923 AN XY: 74384

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.0636

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.159

Alfa AF: 0.185 Hom.: 3797

Bravo AF: 0.171

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.36

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: rs16868941; hg19: chr8-103052377;