8-102072809-G-T

Position:

• chr8-102072809-G-T

Variant summary

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

The XR_007061038.1(LOC124901997):​n.134-4499G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,032 control chromosomes in the GnomAD database, including 2,572 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 0.17 (2572 hom., cov: 32)
• Consequence: LOC124901997 XR_007061038.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828

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]

LOC124901997 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901997	XR_007061038.1	n.134-4499G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCALD	ENST00000521599.5	c.-209-43713C>A		intron_variant		1		ENSP00000428105	P1
NCALD	ENST00000311028.4	c.-210+51428C>A		intron_variant		5		ENSP00000310587	P1
NCALD	ENST00000395923.5	c.-123+51761C>A		intron_variant		5		ENSP00000379256	P1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25876 AN: 151914 Hom.: 2564 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.170 AC: 25914 AN: 152032 Hom.: 2572 Cov.: 32 AF XY: 0.169 AC XY: 12534 AN XY: 74310

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0401

Gnomad4 SAS AF: 0.0670

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.164

Alfa AF: 0.0792 Hom.: 108

Bravo AF: 0.174

Asia WGS AF: 0.0780 AC: 270 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.30
DANN	Benign	0.48

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: rs11784583; hg19: chr8-103085037;