rs2412747

chr15-42994605-T-C

Variant summary

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

The NM_174916.3(UBR1):c.3757+3563A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,112 control chromosomes in the GnomAD database, including 48,830 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 0.79 (48830 hom., cov: 32)
• Consequence: UBR1 NM_174916.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

UBR1 (HGNC:16808): (ubiquitin protein ligase E3 component n-recognin 1) The N-end rule pathway is one proteolytic pathway of the ubiquitin system. The recognition component of this pathway, encoded by this gene, binds to a destabilizing N-terminal residue of a substrate protein and participates in the formation of a substrate-linked multiubiquitin chain. This leads to the eventual degradation of the substrate protein. The protein described in this record has a RING-type zinc finger and a UBR-type zinc finger. Mutations in this gene have been associated with Johanson-Blizzard syndrome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBR1	NM_174916.3	c.3757+3563A>G		intron_variant		ENST00000290650.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBR1	ENST00000290650.9	c.3757+3563A>G		intron_variant		1	NM_174916.3	P1
UBR1	ENST00000566493.1	n.32+3563A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120187 AN: 151994 Hom.: 48827 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.790 AC: 120222 AN: 152112 Hom.: 48830 Cov.: 32 AF XY: 0.793 AC XY: 58961 AN XY: 74354

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.809

Alfa AF: 0.825 Hom.: 7719

Bravo AF: 0.775

Asia WGS AF: 0.775 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.7
Dann	Benign	0.69

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: rs2412747; hg19: chr15-43286803;