rs10211519

Variant names:

• chr2-14830918-A-G
• rs10211519
• ENST00000654007.1:n.857-117623T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-14830918-A-G
• chr2-14830918-A-T

Variant summary

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

The ENST00000654007.1(ENSG00000287291):​n.857-117623T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,978 control chromosomes in the GnomAD database, including 15,805 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 0.44 (15805 hom., cov: 32)
• Consequence: ENSG00000287291 ENST00000654007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 1 publications found

Genes affected

ENSG00000287291 (HGNC:):

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: Labcorp Genetics (formerly Invitae), G2P, Orphanet
• short stature-optic atrophy-Pelger-Huët anomaly syndrome

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654007.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000287291	ENST00000654007.1		n.857-117623T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66346 AN: 151860 Hom.: 15791 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.437 AC: 66407 AN: 151978 Hom.: 15805 Cov.: 32 AF XY: 0.438 AC XY: 32526 AN XY: 74264

African (AFR) AF: 0.636 AC: 26382 AN: 41454

American (AMR) AF: 0.376 AC: 5734 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2068 AN: 5156

South Asian (SAS) AF: 0.383 AC: 1845 AN: 4816

European-Finnish (FIN) AF: 0.458 AC: 4836 AN: 10554

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23155 AN: 67962

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.357 Hom.: 17310

Bravo AF: 0.441

Asia WGS AF: 0.417 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.70
PhyloP100		-0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10211519;

hg19: chr2-14971042;