rs17008097

Variant names:

• chr2-61295935-C-G
• rs17008097
• NM_014709.4:c.4255-645G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-61295935-C-G
• chr2-61295935-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014709.4(USP34):​c.4255-645G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,186 control chromosomes in the GnomAD database, including 2,214 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 0.15 (2214 hom., cov: 32)
• Consequence: USP34 NM_014709.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 4 publications found

Genes affected

USP34 (HGNC:20066): (ubiquitin specific peptidase 34) Enables cysteine-type endopeptidase activity and thiol-dependent deubiquitinase. Involved in positive regulation of canonical Wnt signaling pathway and protein K48-linked deubiquitination. Predicted to be active in cytosol and nucleus. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP34	NM_014709.4	c.4255-645G>C		intron_variant	Intron 30 of 79	ENST00000398571.7	NP_055524.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP34	ENST00000398571.7	c.4255-645G>C		intron_variant	Intron 30 of 79	5	NM_014709.4	ENSP00000381577.2
USP34	ENST00000472706.5	n.208+865G>C		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23252 AN: 152068 Hom.: 2215 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.167

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.153 AC: 23256 AN: 152186 Hom.: 2214 Cov.: 32 AF XY: 0.157 AC XY: 11683 AN XY: 74396

African (AFR) AF: 0.0665 AC: 2762 AN: 41520

American (AMR) AF: 0.259 AC: 3956 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 713 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1564 AN: 5170

South Asian (SAS) AF: 0.364 AC: 1754 AN: 4824

European-Finnish (FIN) AF: 0.102 AC: 1079 AN: 10598

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10824 AN: 67996

Other (OTH) AF: 0.165 AC: 348 AN: 2110

Alfa AF: 0.0662 Hom.: 73

Bravo AF: 0.160

Asia WGS AF: 0.320 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.43
PhyloP100		-2.0
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: rs17008097; hg19: chr2-61523070;