17-22204707-G-C

Position:

• chr17-22204707-G-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The ENST00000584755.2(UBBP4):​n.1012G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.000011 in 1,460,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00018 (0 hom., cov: 29)
  • Exomes 𝑓: 0.000011 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBBP4 ENST00000584755.2 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.89

Genes affected

UBBP4 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP6: Variant 17-22204707-G-C is Benign according to our data. Variant chr17-22204707-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3234294.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBBP4	NR_144546.2	n.1012G>C		non_coding_transcript_exon_variant	2/2
UBBP4	NR_176224.1	n.970G>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBBP4	ENST00000584755.2	n.1012G>C		non_coding_transcript_exon_variant	2/2	1
UBBP4	ENST00000583708.6	n.615G>C		non_coding_transcript_exon_variant	1/1	6
UBBP4	ENST00000648259.1	n.977G>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 22 AN: 124888 Hom.: 0 Cov.: 29 FAILED QC

Gnomad AFR AF: 0.000248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000807

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000490

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000134

Gnomad MID AF: 0.00568

Gnomad NFE AF: 0.000152

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000802 AC: 2 AN: 249252 Hom.: 0 AF XY: 0.0000148 AC XY: 2 AN XY: 134874

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000659

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000110 AC: 16 AN: 1460388 Hom.: 0 Cov.: 35 AF XY: 0.0000165 AC XY: 12 AN XY: 726386

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000756

Gnomad4 SAS exome AF: 0.0000582

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000540

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000184 AC: 23 AN: 124984 Hom.: 0 Cov.: 29 AF XY: 0.000132 AC XY: 8 AN XY: 60400

Gnomad4 AFR AF: 0.000278

Gnomad4 AMR AF: 0.0000806

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000491

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000134

Gnomad4 NFE AF: 0.000152

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000237 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2024

UBBP4: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	10
DANN	Benign	0.46
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs761552039; hg19: chr17-21731313;