chr3-196361593-G-T

Variant names:

• chr3-196361593-G-T
• rs6764533
• NM_015562.2:c.1308+251C>A

Variant summary

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

The NM_015562.2(UBXN7):​c.1308+251C>A 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: 32)
• Consequence: UBXN7 NM_015562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 11 publications found

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

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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN7	NM_015562.2	c.1308+251C>A		intron_variant	Intron 10 of 10	ENST00000296328.9	NP_056377.1
UBXN7	XM_011512671.3	c.864+251C>A		intron_variant	Intron 9 of 9		XP_011510973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBXN7	ENST00000296328.9	c.1308+251C>A		intron_variant	Intron 10 of 10	1	NM_015562.2	ENSP00000296328.4
UBXN7	ENST00000428095.1	c.822+251C>A		intron_variant	Intron 6 of 6	1		ENSP00000397256.1
UBXN7	ENST00000381887.8	c.1242+251C>A		intron_variant	Intron 9 of 9	3		ENSP00000371311.4
UBXN7	ENST00000429160.1	n.*932+251C>A		intron_variant	Intron 9 of 9	2		ENSP00000397238.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.60
PhyloP100		0.34

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

Other links and lift over

dbSNP: rs6764533; hg19: chr3-196088464;