rs6432474

Variant names:

• chr2-14808237-A-C
• rs6432474
• ENST00000654007.1:n.857-94942T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-14808237-A-C
• chr2-14808237-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.857-94942T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,080 control chromosomes in the GnomAD database, including 12,548 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 0.40 (12548 hom., cov: 33)
• Consequence: ENSG00000287291 ENST00000654007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37
• 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: 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NBAS	XR_007076390.1	n.7016-29090T>G		intron_variant	Intron 53 of 53

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287291	ENST00000654007.1	n.857-94942T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60413 AN: 151962 Hom.: 12531 Cov.: 33

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.398 AC: 60479 AN: 152080 Hom.: 12548 Cov.: 33 AF XY: 0.400 AC XY: 29761 AN XY: 74320

African (AFR) AF: 0.507 AC: 21028 AN: 41478

American (AMR) AF: 0.355 AC: 5427 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1143 AN: 3472

East Asian (EAS) AF: 0.383 AC: 1980 AN: 5164

South Asian (SAS) AF: 0.397 AC: 1913 AN: 4822

European-Finnish (FIN) AF: 0.458 AC: 4839 AN: 10558

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22988 AN: 67988

Other (OTH) AF: 0.374 AC: 790 AN: 2112

Alfa AF: 0.332 Hom.: 4359

Bravo AF: 0.395

Asia WGS AF: 0.410 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.84
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs6432474; hg19: chr2-14948361;