3-196351556-C-T

Position:

• chr3-196351556-C-T

Variant summary

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

The NM_015562.2(UBXN7):​c.*5129G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,170 control chromosomes in the GnomAD database, including 59,262 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 0.88 (59262 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: UBXN7 NM_015562.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517

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 = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBXN7	NM_015562.2	c.*5129G>A		3_prime_UTR_variant	11/11	ENST00000296328.9	NP_056377.1
UBXN7	XM_011512671.3	c.*5129G>A		3_prime_UTR_variant	10/10		XP_011510973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBXN7	ENST00000296328	c.*5129G>A		3_prime_UTR_variant	11/11	1	NM_015562.2	ENSP00000296328.4

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133787 AN: 152052 Hom.: 59214 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.873

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.880 AC: 133887 AN: 152170 Hom.: 59262 Cov.: 31 AF XY: 0.880 AC XY: 65436 AN XY: 74386

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.910

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.873

Alfa AF: 0.846 Hom.: 57287

Bravo AF: 0.889

Asia WGS AF: 0.926 AC: 3218 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	0.78
DANN	Benign	0.49

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: rs6774852; hg19: chr3-196078427;