rs6764533

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-196361593-G-A
• chr3-196361593-G-C
• chr3-196361593-G-T

Variant summary

Our verdict is Benign. The variant received -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
• 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: 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 = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN7	NM_015562.2	c.1308+251C>T		intron_variant	Intron 10 of 10	ENST00000296328.9	NP_056377.1
UBXN7	XM_011512671.3	c.864+251C>T		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>T		intron_variant	Intron 10 of 10	1	NM_015562.2	ENSP00000296328.4
UBXN7	ENST00000428095.1	c.822+251C>T		intron_variant	Intron 6 of 6	1		ENSP00000397256.1
UBXN7	ENST00000381887.8	c.1242+251C>T		intron_variant	Intron 9 of 9	3		ENSP00000371311.4
UBXN7	ENST00000429160.1	n.*932+251C>T		intron_variant	Intron 9 of 9	2		ENSP00000397238.1

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

African (AFR) AF: 0.193 AC: 8005 AN: 41454

American (AMR) AF: 0.454 AC: 6921 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1170 AN: 3468

East Asian (EAS) AF: 0.826 AC: 4277 AN: 5180

South Asian (SAS) AF: 0.312 AC: 1504 AN: 4818

European-Finnish (FIN) AF: 0.294 AC: 3099 AN: 10554

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24605 AN: 67976

Other (OTH) AF: 0.351 AC: 742 AN: 2112

Alfa AF: 0.346 Hom.: 15398

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
PhyloP100		0.34
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: rs6764533; hg19: chr3-196088464;