2-135741596-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_163478.1(LOC107985946):​n.1049C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

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>G		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>G		intron	N/A
	ENSG00000308733	ENST00000836083.1		n.81+19C>G		intron	N/A
	UBXN4	ENST00000415164.5	TSL:4	c.-334G>C		upstream_gene	N/A	ENSP00000401748.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 173962 Hom.: 0 Cov.: 1 AF XY: 0.00 AC XY: 0 AN XY: 89514

African (AFR) AF: 0.00 AC: 0 AN: 4446

American (AMR) AF: 0.00 AC: 0 AN: 4820

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6256

East Asian (EAS) AF: 0.00 AC: 0 AN: 12050

South Asian (SAS) AF: 0.00 AC: 0 AN: 12548

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12160

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 888

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 109518

Other (OTH) AF: 0.00 AC: 0 AN: 11276

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.3
DANN	Benign	0.67
PhyloP100		-0.23
PromoterAI		-0.0018	Neutral

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;