chr1-229628627-C-T

Position:

• chr1-229628627-C-T

Variant summary

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

The NM_014777.4(URB2):​c.126+868C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 151,976 control chromosomes in the GnomAD database, including 1,961 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 0.13 (1961 hom., cov: 32)
• Consequence: URB2 NM_014777.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

Genes affected

URB2 (HGNC:28967): (URB2 ribosome biogenesis homolog) Predicted to be involved in ribosome biogenesis. Located in aggresome; midbody; and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
URB2	NM_014777.4	c.126+868C>T		intron_variant		ENST00000258243.7	NP_055592.2
URB2	NM_001314021.2	c.126+868C>T		intron_variant			NP_001300950.1
URB2	XM_005273360.3	c.126+868C>T		intron_variant			XP_005273417.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
URB2	ENST00000258243.7	c.126+868C>T		intron_variant		1	NM_014777.4	ENSP00000258243.2

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19778 AN: 151858 Hom.: 1956 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.0765

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.0913

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0595

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.130 AC: 19806 AN: 151976 Hom.: 1961 Cov.: 32 AF XY: 0.137 AC XY: 10162 AN XY: 74282

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.0765

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.0916

Gnomad4 FIN AF: 0.0857

Gnomad4 NFE AF: 0.0595

Gnomad4 OTH AF: 0.126

Alfa AF: 0.117 Hom.: 307

Bravo AF: 0.150

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.99
DANN	Benign	0.46

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: rs3767331; hg19: chr1-229764374;