2-15053695-G-C

Variant names:

• chr2-15053695-G-C
• rs10206283
• XM_017004317.2:c.*49-55471C>G

Variant summary

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

The XR_007076390.1(NBAS):​n.7015+30170C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,630 control chromosomes in the GnomAD database, including 6,705 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 (6705 hom., cov: 31)
• Consequence: NBAS XR_007076390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• infantile liver failure syndrome 2

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae)
• short stature-optic atrophy-Pelger-Huët anomaly syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Illumina, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.399 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43319 AN: 151512 Hom.: 6702 Cov.: 31

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.286 AC: 43344 AN: 151630 Hom.: 6705 Cov.: 31 AF XY: 0.283 AC XY: 20953 AN XY: 74084

African (AFR) AF: 0.404 AC: 16713 AN: 41322

American (AMR) AF: 0.216 AC: 3289 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1030 AN: 3460

East Asian (EAS) AF: 0.0982 AC: 506 AN: 5152

South Asian (SAS) AF: 0.251 AC: 1198 AN: 4774

European-Finnish (FIN) AF: 0.263 AC: 2769 AN: 10534

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16943 AN: 67856

Other (OTH) AF: 0.276 AC: 579 AN: 2098

Alfa AF: 0.147 Hom.: 269

Bravo AF: 0.286

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.50
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs10206283; hg19: chr2-15193819;