chr2-15062556-A-G

Variant names:

• chr2-15062556-A-G
• rs1862110
• XM_017004317.2:c.*49-64332T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_017004317.2(NBAS):​c.*49-64332T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,050 control chromosomes in the GnomAD database, including 21,893 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 0.51 (21893 hom., cov: 32)
• Consequence: NBAS XM_017004317.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50
• Publications: 5 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, Labcorp Genetics (formerly Invitae), G2P
• short stature-optic atrophy-Pelger-Huët anomaly syndrome

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77247 AN: 151932 Hom.: 21893 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.508 AC: 77258 AN: 152050 Hom.: 21893 Cov.: 32 AF XY: 0.511 AC XY: 38002 AN XY: 74306

African (AFR) AF: 0.234 AC: 9716 AN: 41504

American (AMR) AF: 0.574 AC: 8773 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2289 AN: 3468

East Asian (EAS) AF: 0.580 AC: 2986 AN: 5152

South Asian (SAS) AF: 0.578 AC: 2786 AN: 4818

European-Finnish (FIN) AF: 0.611 AC: 6442 AN: 10548

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42416 AN: 67974

Other (OTH) AF: 0.548 AC: 1153 AN: 2104

Alfa AF: 0.513 Hom.: 3644

Bravo AF: 0.494

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	21
DANN	Benign	0.78
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs1862110; hg19: chr2-15202680;