rs6724694

Variant names:

• chr2-14812061-T-C
• rs6724694
• ENST00000654007.1:n.857-98766A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-14812061-T-C
• chr2-14812061-T-G

Variant summary

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

The ENST00000654007.1(ENSG00000287291):​n.857-98766A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,010 control chromosomes in the GnomAD database, including 13,265 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 0.41 (13265 hom., cov: 32)
• Consequence: ENSG00000287291 ENST00000654007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 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.857-98766A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61822 AN: 151892 Hom.: 13245 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.407 AC: 61893 AN: 152010 Hom.: 13265 Cov.: 32 AF XY: 0.409 AC XY: 30415 AN XY: 74282

African (AFR) AF: 0.538 AC: 22303 AN: 41438

American (AMR) AF: 0.361 AC: 5518 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1147 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1988 AN: 5160

South Asian (SAS) AF: 0.398 AC: 1916 AN: 4820

European-Finnish (FIN) AF: 0.459 AC: 4843 AN: 10560

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

European-Non Finnish (NFE) AF: 0.338 AC: 23002 AN: 67972

Other (OTH) AF: 0.380 AC: 801 AN: 2110

Alfa AF: 0.354 Hom.: 37358

Bravo AF: 0.406

Asia WGS AF: 0.413 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.80
PhyloP100		-0.68

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: rs6724694;

hg19: chr2-14952185;