rs544821

Variant names:

• chr8-101888897-A-C
• rs544821
• ENST00000521599.5:c.-20+26912T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-101888897-A-C
• chr8-101888897-A-T

Variant summary

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

The NM_001040624.2(NCALD):​c.-106-1670T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,050 control chromosomes in the GnomAD database, including 15,378 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 0.40 (15378 hom., cov: 32)
• Consequence: NCALD NM_001040624.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 2 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCALD	NM_001040624.2		c.-106-1670T>G		intron	N/A	NP_001035714.1
	NCALD	NM_001040625.2		c.-20+26912T>G		intron	N/A	NP_001035715.1
	NCALD	NM_001040626.2		c.-106-1670T>G		intron	N/A	NP_001035716.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCALD	ENST00000521599.5	TSL:1	c.-20+26912T>G		intron	N/A	ENSP00000428105.1
	NCALD	ENST00000311028.4	TSL:5	c.-106-1670T>G		intron	N/A	ENSP00000310587.3
	NCALD	ENST00000395923.5	TSL:5	c.-20+26912T>G		intron	N/A	ENSP00000379256.1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60206 AN: 151932 Hom.: 15333 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.397 AC: 60308 AN: 152050 Hom.: 15378 Cov.: 32 AF XY: 0.394 AC XY: 29298 AN XY: 74344

African (AFR) AF: 0.717 AC: 29720 AN: 41446

American (AMR) AF: 0.405 AC: 6198 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2041 AN: 5178

South Asian (SAS) AF: 0.325 AC: 1559 AN: 4798

European-Finnish (FIN) AF: 0.210 AC: 2222 AN: 10582

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16657 AN: 67968

Other (OTH) AF: 0.365 AC: 770 AN: 2112

Alfa AF: 0.271 Hom.: 4290

Bravo AF: 0.428

Asia WGS AF: 0.425 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.3
DANN	Benign	0.67
PhyloP100		0.22
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: rs544821; hg19: chr8-102901125;