2-135741596-G-T

Variant names:

• chr2-135741596-G-T
• rs1438307
• NR_163478.1:n.1049C>A

Variant summary

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

The NR_163478.1(LOC107985946):​n.1049C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 325,492 control chromosomes in the GnomAD database, including 63,511 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 0.53 (25504 hom., cov: 33)
  • Exomes 𝑓: 0.64 (38007 hom.)
• Consequence: LOC107985946 NR_163478.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 18 publications found

Genes affected

LOC107985946 (HGNC:):

UBXN4 (HGNC:14860): (UBX domain protein 4) UBXD2 is an integral membrane protein of the endoplasmic reticulum (ER) that binds valosin-containing protein (VCP; MIM 601023) and promotes ER-associated protein degradation (ERAD) (Liang et al., 2006 [PubMed 16968747]).[supplied by OMIM, Mar 2008]

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 (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_163478.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC107985946	NR_163478.1		n.1049C>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308733	ENST00000836082.1		n.93+19C>A		intron	N/A
	ENSG00000308733	ENST00000836083.1		n.81+19C>A		intron	N/A
	UBXN4	ENST00000415164.5	TSL:4	c.-334G>T		upstream_gene	N/A	ENSP00000401748.1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80260 AN: 152044 Hom.: 25502 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.481

GnomAD4 exome AF: 0.637 AC: 110447 AN: 173330 Hom.: 38007 Cov.: 1 AF XY: 0.627 AC XY: 55910 AN XY: 89218

African (AFR) AF: 0.220 AC: 976 AN: 4432

American (AMR) AF: 0.462 AC: 2212 AN: 4792

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 2320 AN: 6234

East Asian (EAS) AF: 0.438 AC: 5258 AN: 12008

South Asian (SAS) AF: 0.430 AC: 5371 AN: 12500

European-Finnish (FIN) AF: 0.736 AC: 8923 AN: 12120

Middle Eastern (MID) AF: 0.321 AC: 285 AN: 888

European-Non Finnish (NFE) AF: 0.719 AC: 78436 AN: 109132

Other (OTH) AF: 0.594 AC: 6666 AN: 11224

GnomAD4 genome AF: 0.527 AC: 80264 AN: 152162 Hom.: 25504 Cov.: 33 AF XY: 0.519 AC XY: 38587 AN XY: 74392

African (AFR) AF: 0.220 AC: 9145 AN: 41534

American (AMR) AF: 0.438 AC: 6699 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1285 AN: 3468

East Asian (EAS) AF: 0.378 AC: 1949 AN: 5150

South Asian (SAS) AF: 0.386 AC: 1864 AN: 4826

European-Finnish (FIN) AF: 0.733 AC: 7767 AN: 10602

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.732 AC: 49757 AN: 67978

Other (OTH) AF: 0.476 AC: 1005 AN: 2110

Alfa AF: 0.637 Hom.: 72299

Bravo AF: 0.496

Asia WGS AF: 0.393 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		-0.23
PromoterAI		-0.0046	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1438307; hg19: chr2-136499166;