17-22180454-A-G

Position:

• chr17-22180454-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_176224.1(UBBP4):​n.160-1085A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,096 control chromosomes in the GnomAD database, including 2,805 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 0.18 (2805 hom., cov: 32)
• Consequence: UBBP4 NR_176224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

UBBP4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBBP4	NR_176224.1	n.160-1085A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBBP4	ENST00000648259.1	n.167-1085A>G		intron_variant
UBBP4	ENST00000688301.1	n.158-23633A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27474 AN: 151976 Hom.: 2797 Cov.: 32

Gnomad AFR AF: 0.0951

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.181 AC: 27495 AN: 152096 Hom.: 2805 Cov.: 32 AF XY: 0.180 AC XY: 13400 AN XY: 74366

Gnomad4 AFR AF: 0.0952

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.214

Alfa AF: 0.202 Hom.: 3039

Bravo AF: 0.171

Asia WGS AF: 0.223 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1975974; hg19: chr17-21707060;