rs2031011

Positions:

• chr2-15408266-T-C

Variant summary

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

The NM_015909.4(NBAS):​c.2938-5965A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,104 control chromosomes in the GnomAD database, including 26,776 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 0.55 (26776 hom., cov: 32)
• Consequence: NBAS NM_015909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610

Genes affected

NBAS (HGNC:15625): (NBAS subunit of NRZ tethering complex) This gene encodes a protein with two leucine zipper domains, a ribosomal protein S14 signature domain and a Sec39 like domain. The protein is thought to be involved in Golgi-to-ER transport. Mutations in this gene are associated with short stature, optic nerve atrophy, and Pelger-Huet anomaly. [provided by RefSeq, Oct 2012]

NBAS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBAS	NM_015909.4	c.2938-5965A>G		intron_variant		ENST00000281513.10	NP_056993.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NBAS	ENST00000281513.10	c.2938-5965A>G		intron_variant		1	NM_015909.4	ENSP00000281513.5

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84268 AN: 151986 Hom.: 26791 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.554 AC: 84267 AN: 152104 Hom.: 26776 Cov.: 32 AF XY: 0.549 AC XY: 40822 AN XY: 74374

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.614

Alfa AF: 0.690 Hom.: 50398

Bravo AF: 0.540

Asia WGS AF: 0.340 AC: 1183 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	11
DANN	Benign	0.93

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: rs2031011; hg19: chr2-15548390;