rs6764533

chr3-196361593-G-Achr3-196361593-G-Cchr3-196361593-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015562.2(UBXN7):c.1308+251C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,026 control chromosomes in the GnomAD database, including 9,674 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 0.33 (9674 hom., cov: 32)
• Consequence: UBXN7 NM_015562.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBXN7	NM_015562.2	c.1308+251C>T		intron_variant		ENST00000296328.9
UBXN7	XM_011512671.3	c.864+251C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBXN7	ENST00000296328.9	c.1308+251C>T		intron_variant		1	NM_015562.2	P1
UBXN7	ENST00000428095.1	c.822+251C>T		intron_variant		1
UBXN7	ENST00000429160.1	c.*932+251C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50626 AN: 151908 Hom.: 9660 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.333 AC: 50660 AN: 152026 Hom.: 9674 Cov.: 32 AF XY: 0.334 AC XY: 24838 AN XY: 74288

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.351

Alfa AF: 0.350 Hom.: 9341

Bravo AF: 0.345

Asia WGS AF: 0.524 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.9
Dann	Benign	0.51

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: rs6764533; hg19: chr3-196088464;