3-196391750-A-T

Variant summary

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

The NM_015562.2(UBXN7):c.468+63T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 1,215,114 control chromosomes in the GnomAD database, including 86,339 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 0.38 (11433 hom., cov: 29)
  • Exomes 𝑓: 0.36 (74906 hom.)
• 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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.468+63T>A		intron_variant		ENST00000296328.9
UBXN7	XM_011512671.3	c.24+63T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBXN7	ENST00000296328.9	c.468+63T>A		intron_variant		1	NM_015562.2	P1
UBXN7	ENST00000428095.1	c.-18-19708T>A		intron_variant		1
UBXN7	ENST00000429160.1	c.*92+63T>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57074 AN: 151494 Hom.: 11415 Cov.: 29

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.377

GnomAD4 exome AF: 0.360 AC: 382720 AN: 1063504 Hom.: 74906 AF XY: 0.357 AC XY: 194026 AN XY: 543106

Gnomad4 AFR exome AF: 0.329

Gnomad4 AMR exome AF: 0.491

Gnomad4 ASJ exome AF: 0.331

Gnomad4 EAS exome AF: 0.843

Gnomad4 SAS exome AF: 0.291

Gnomad4 FIN exome AF: 0.296

Gnomad4 NFE exome AF: 0.345

Gnomad4 OTH exome AF: 0.356

GnomAD4 genome AF: 0.377 AC: 57124 AN: 151610 Hom.: 11433 Cov.: 29 AF XY: 0.376 AC XY: 27849 AN XY: 74086

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.382

Alfa AF: 0.363 Hom.: 1291

Bravo AF: 0.395

Asia WGS AF: 0.529 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.32
Dann	Benign	0.17

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;