rs6583305

Variant names:

• chr3-196391750-A-C
• rs6583305
• NM_015562.2:c.468+63T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-196391750-A-C
• chr3-196391750-A-G
• chr3-196391750-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_015562.2(UBXN7):​c.468+63T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000748 in 1,068,912 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 29)
  • Exomes 𝑓: 0.0000075 (0 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS2: High AC in GnomAdExome4 at 8 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN7	NM_015562.2	c.468+63T>G		intron_variant	Intron 5 of 10	ENST00000296328.9	NP_056377.1
UBXN7	XM_011512671.3	c.24+63T>G		intron_variant	Intron 4 of 9		XP_011510973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBXN7	ENST00000296328.9	c.468+63T>G		intron_variant	Intron 5 of 10	1	NM_015562.2	ENSP00000296328.4
UBXN7	ENST00000428095.1	c.-18-19708T>G		intron_variant	Intron 1 of 6	1		ENSP00000397256.1
UBXN7	ENST00000429160.1	n.*92+63T>G		intron_variant	Intron 4 of 9	2		ENSP00000397238.1
UBXN7	ENST00000381887.7	c.*88T>G		downstream_gene_variant		3		ENSP00000371311.4

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome AF: 0.00000748 AC: 8 AN: 1068912 Hom.: 0 AF XY: 0.00000916 AC XY: 5 AN XY: 545670

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000102

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.41
DANN	Benign	0.20

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;