rs12767760

chr10-97535040-G-A

Variant summary

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

The NM_024954.5(UBTD1):c.71-32874G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,118 control chromosomes in the GnomAD database, including 33,095 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 0.62 (33095 hom., cov: 32)
• Consequence: UBTD1 NM_024954.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

Genes affected

UBTD1 (HGNC:25683): (ubiquitin domain containing 1) The degradation of many proteins is carried out by the ubiquitin pathway in which proteins are targeted for degradation by covalent conjugation of the polypeptide ubiquitin. This gene encodes a protein that belongs to the ubiquitin family of proteins. The encoded protein is thought to regulate E2 ubiquitin conjugating enzymes belonging to the UBE2D family. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBTD1	NM_024954.5	c.71-32874G>A		intron_variant		ENST00000370664.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBTD1	ENST00000370664.4	c.71-32874G>A		intron_variant		1	NM_024954.5	P1

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94651 AN: 152000 Hom.: 33090 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.622 AC: 94660 AN: 152118 Hom.: 33095 Cov.: 32 AF XY: 0.623 AC XY: 46355 AN XY: 74376

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.652

Alfa AF: 0.760 Hom.: 58924

Bravo AF: 0.596

Asia WGS AF: 0.466 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.8
Dann	Benign	0.41

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: rs12767760; hg19: chr10-99294797;