17-22204923-T-C

Position:

• chr17-22204923-T-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.1228T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00081 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000043 (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: 1.67

Genes affected

UBBP4 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP6: Variant 17-22204923-T-C is Benign according to our data. Variant chr17-22204923-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3234342.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.1228T>C		non_coding_transcript_exon_variant	2/2
UBBP4	NR_176224.1	n.1186T>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.1228T>C		non_coding_transcript_exon_variant	2/2	1
UBBP4	ENST00000583708.6	n.831T>C		non_coding_transcript_exon_variant	1/1	6
UBBP4	ENST00000648259.1	n.1193T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 111 AN: 135674 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.000997

Gnomad AMI AF: 0.00256

Gnomad AMR AF: 0.000216

Gnomad ASJ AF: 0.000627

Gnomad EAS AF: 0.00323

Gnomad SAS AF: 0.00148

Gnomad FIN AF: 0.000534

Gnomad MID AF: 0.0183

Gnomad NFE AF: 0.000598

Gnomad OTH AF: 0.00107

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000431 AC: 62 AN: 1436924 Hom.: 0 Cov.: 34 AF XY: 0.0000532 AC XY: 38 AN XY: 714740

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000975

Gnomad4 ASJ exome AF: 0.0000393

Gnomad4 EAS exome AF: 0.0000791

Gnomad4 SAS exome AF: 0.000191

Gnomad4 FIN exome AF: 0.0000189

Gnomad4 NFE exome AF: 0.0000273

Gnomad4 OTH exome AF: 0.000118

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000810 AC: 110 AN: 135776 Hom.: 0 Cov.: 32 AF XY: 0.000644 AC XY: 43 AN XY: 66742

Gnomad4 AFR AF: 0.000995

Gnomad4 AMR AF: 0.000215

Gnomad4 ASJ AF: 0.000627

Gnomad4 EAS AF: 0.00324

Gnomad4 SAS AF: 0.00148

Gnomad4 FIN AF: 0.000534

Gnomad4 NFE AF: 0.000598

Gnomad4 OTH AF: 0.00106

Alfa AF: 0.00723 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	-0.70
CADD	Benign	14
DANN	Benign	0.36
RBP_binding_hub_radar		1.0
RBP_regulation_power_radar		2.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs745804544; hg19: chr17-21731529;