3-196391750-A-G

Variant names:

• chr3-196391750-A-G
• rs6583305
• NM_015562.2:c.468+63T>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015562.2(UBXN7):​c.468+63T>C variant causes a intron 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: 29)
• Consequence: UBXN7 NM_015562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

UBXN7 (HGNC:29119): (UBX domain protein 7) Enables ubiquitin binding activity and ubiquitin protein ligase binding activity. Located in nuclear body. Part of VCP-NPL4-UFD1 AAA ATPase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN7	NM_015562.2	c.468+63T>C		intron_variant	Intron 5 of 10	ENST00000296328.9	NP_056377.1
UBXN7	XM_011512671.3	c.24+63T>C		intron_variant	Intron 4 of 9		XP_011510973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBXN7	ENST00000296328.9	c.468+63T>C		intron_variant	Intron 5 of 10	1	NM_015562.2	ENSP00000296328.4
UBXN7	ENST00000428095.1	c.-18-19708T>C		intron_variant	Intron 1 of 6	1		ENSP00000397256.1
UBXN7	ENST00000429160.1	n.*92+63T>C		intron_variant	Intron 4 of 9	2		ENSP00000397238.1
UBXN7	ENST00000381887.7	c.*88T>C		downstream_gene_variant		3		ENSP00000371311.4

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.45
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6583305; hg19: chr3-196118621;