8-102124496-GCCC-GCCCCCCCCCCCCCCCC

Variant names:

• chr8-102124496-G-GCCCCCCCCCCCCC
• rs1046926270
• NM_001040630.2:c.-123+73_-123+74insGGGGGGGGGGGGG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001040630.2(NCALD):​c.-123+73_-123+74insGGGGGGGGGGGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000026 (0 hom., cov: 25)
  • Failed GnomAD Quality Control
• Consequence: NCALD NM_001040630.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCALD	NM_001040630.2	c.-123+73_-123+74insGGGGGGGGGGGGG		intron_variant	Intron 1 of 5		NP_001035720.1
NCALD	XM_047422315.1	c.-210+73_-210+74insGGGGGGGGGGGGG		intron_variant	Intron 1 of 6		XP_047278271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCALD	ENST00000395923.5	c.-123+73_-123+74insGGGGGGGGGGGGG		intron_variant	Intron 1 of 5	5		ENSP00000379256.1
NCALD	ENST00000522206.5	c.-241+130_-241+131insGGGGGGGGGGGGG		intron_variant	Intron 1 of 4	4		ENSP00000429296.1
NCALD	ENST00000522078.5	c.-210+73_-210+74insGGGGGGGGGGGGG		intron_variant	Intron 1 of 4	4		ENSP00000429162.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2 AN: 75836 Hom.: 0 Cov.: 25 FAILED QC

Gnomad AFR AF: 0.0000422

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000317

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000264 AC: 2 AN: 75882 Hom.: 0 Cov.: 25 AF XY: 0.0000546 AC XY: 2 AN XY: 36632

Gnomad4 AFR AF: 0.0000421

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000318

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1046926270; hg19: chr8-103136724;