dbSNP rs1438307: LOC107985946:n.1049C>T (chr2-135741596-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NR_163478.1(LOC107985946):n.1049C>T 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 0.00000575 in 173,962 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000057 ( 0 hom. )

Consequence

LOC107985946
NR_163478.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.226

Publications

0 publications found

Variant links:

Genes affected

LOC107985946 (HGNC:):

LOC107985946 links:

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]

UBXN4 links:

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ACMG classification

Classification was made for transcript

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=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985946	NR_163478.1 link	n.1049C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000308733	ENST00000836082.1 link	n.93+19C>T	intron_variant	Intron 1 of 1
ENSG00000308733	ENST00000836083.1 link	n.81+19C>T	intron_variant	Intron 1 of 2
UBXN4	ENST00000415164.5 link	c.-334G>A	upstream_gene_variant		4	ENSP00000401748.1	C9JLR4
UBXN4	ENST00000426921.5 link	n.-334G>A	upstream_gene_variant		4	ENSP00000410516.1	F8WB86

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000575

AC:

AN:

173962

Hom.:

Cov.:

AF XY:

0.0000112

AC XY:

AN XY:

89514

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

4446

American (AMR)

AF:

0.00

AC:

AN:

4820

Ashkenazi Jewish (ASJ)

AF:

0.000160

AC:

AN:

6256

East Asian (EAS)

AF:

0.00

AC:

AN:

12050

South Asian (SAS)

AF:

0.00

AC:

AN:

12548

European-Finnish (FIN)

AF:

0.00

AC:

AN:

12160

Middle Eastern (MID)

AF:

0.00

AC:

AN:

888

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

109518

Other (OTH)

AF:

0.00

AC:

AN:

11276

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.4

(source)

DANN

Benign

0.91

PhyloP100

-0.23

PromoterAI

-0.017

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over