3-196351556-C-T

Variant names:

• chr3-196351556-C-T
• rs6774852
• NM_015562.2:c.*5129G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015562.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBXN7	NM_015562.2	MANE Select	c.*5129G>A		3_prime_UTR	Exon 11 of 11	NP_056377.1	O94888

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBXN7	ENST00000296328.9	TSL:1 MANE Select	c.*5129G>A		3_prime_UTR	Exon 11 of 11	ENSP00000296328.4	O94888
	UBXN7	ENST00000381887.8	TSL:3	c.*5129G>A		3_prime_UTR	Exon 10 of 10	ENSP00000371311.4	H7BYF4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.971 AC: 40328 AN: 41552

American (AMR) AF: 0.861 AC: 13153 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3205 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5075 AN: 5182

South Asian (SAS) AF: 0.910 AC: 4390 AN: 4824

European-Finnish (FIN) AF: 0.782 AC: 8244 AN: 10548

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56657 AN: 68006

Other (OTH) AF: 0.873 AC: 1843 AN: 2112

Alfa AF: 0.858 Hom.: 109314

Bravo AF: 0.889

Asia WGS AF: 0.926 AC: 3218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.78
DANN	Benign	0.49
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

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: rs6774852; hg19: chr3-196078427;