rs501344

Variant names:

• chr8-102102345-G-A
• rs501344
• ENST00000521599.5:c.-210+21892C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-102102345-G-A
• chr8-102102345-G-C

Variant summary

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

The NM_001040624.2(NCALD):​c.-297+21892C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,892 control chromosomes in the GnomAD database, including 7,715 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 0.31 (7715 hom., cov: 32)
• Consequence: NCALD NM_001040624.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 5 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]

ENSG00000310378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCALD	NM_001040624.2		c.-297+21892C>T		intron	N/A	NP_001035714.1
	NCALD	NM_001040625.2		c.-210+21892C>T		intron	N/A	NP_001035715.1
	NCALD	NM_001040626.2		c.-210+21892C>T		intron	N/A	NP_001035716.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCALD	ENST00000521599.5	TSL:1	c.-210+21892C>T		intron	N/A	ENSP00000428105.1
	NCALD	ENST00000311028.4	TSL:5	c.-210+21892C>T		intron	N/A	ENSP00000310587.3
	NCALD	ENST00000395923.5	TSL:5	c.-123+22225C>T		intron	N/A	ENSP00000379256.1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46830 AN: 151776 Hom.: 7717 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.308 AC: 46856 AN: 151892 Hom.: 7715 Cov.: 32 AF XY: 0.309 AC XY: 22916 AN XY: 74226

African (AFR) AF: 0.188 AC: 7799 AN: 41476

American (AMR) AF: 0.284 AC: 4342 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1157 AN: 3466

East Asian (EAS) AF: 0.432 AC: 2217 AN: 5134

South Asian (SAS) AF: 0.397 AC: 1903 AN: 4798

European-Finnish (FIN) AF: 0.304 AC: 3204 AN: 10542

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25172 AN: 67890

Other (OTH) AF: 0.324 AC: 682 AN: 2108

Alfa AF: 0.344 Hom.: 16640

Bravo AF: 0.303

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		0.093
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

Other links and lift over

dbSNP: rs501344; hg19: chr8-103114573;