20-33675156-G-A

Position:

• chr20-33675156-G-A

Variant summary

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

The XM_047440369.1(NECAB3):​c.-331C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,806 control chromosomes in the GnomAD database, including 6,595 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 0.29 (6539 hom., cov: 28)
  • Exomes 𝑓: 0.26 (56 hom.)
• Consequence: NECAB3 XM_047440369.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

NECAB3 (HGNC:15851): (N-terminal EF-hand calcium binding protein 3) The protein encoded by this gene interacts with the amino-terminal domain of the neuron-specific X11-like protein (X11L), inhibits the association of X11L with amyloid precursor protein through a non-competitive mechanism, and abolishes the suppression of beta-amyloid production by X11L. This protein, together with X11L, may play an important role in the regulatory system of amyloid precursor protein metabolism and beta-amyloid generation. The protein is phosphorylated by NIMA-related expressed kinase 2, and localizes to the Golgi apparatus. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000271803 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NECAB3	XM_047440369.1	c.-331C>T		5_prime_UTR_variant	1/12		XP_047296325.1
NECAB3	XM_047440370.1	c.-331C>T		5_prime_UTR_variant	1/13		XP_047296326.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000271803	ENST00000606866.1	n.312-96G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.291 AC: 43726 AN: 150144 Hom.: 6538 Cov.: 28

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.263 AC: 406 AN: 1546 Hom.: 56 AF XY: 0.269 AC XY: 215 AN XY: 798

Gnomad4 AFR exome AF: 0.310

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.158

Gnomad4 EAS exome AF: 0.304

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.338

Gnomad4 NFE exome AF: 0.249

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.291 AC: 43737 AN: 150260 Hom.: 6539 Cov.: 28 AF XY: 0.293 AC XY: 21469 AN XY: 73248

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.299

Alfa AF: 0.281 Hom.: 6358

Bravo AF: 0.283

Asia WGS AF: 0.293 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3213183; hg19: chr20-32262962;