rs12767760

Variant names:

• chr10-97535040-G-A
• rs12767760
• NM_024954.5:c.71-32874G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024954.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBTD1	NM_024954.5	MANE Select	c.71-32874G>A		intron	N/A	NP_079230.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBTD1	ENST00000370664.4	TSL:1 MANE Select	c.71-32874G>A		intron	N/A	ENSP00000359698.3

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

African (AFR) AF: 0.293 AC: 12159 AN: 41444

American (AMR) AF: 0.666 AC: 10183 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2506 AN: 3466

East Asian (EAS) AF: 0.419 AC: 2168 AN: 5174

South Asian (SAS) AF: 0.574 AC: 2770 AN: 4826

European-Finnish (FIN) AF: 0.815 AC: 8643 AN: 10602

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54091 AN: 68002

Other (OTH) AF: 0.652 AC: 1377 AN: 2112

Alfa AF: 0.709 Hom.: 84151

Bravo AF: 0.596

Asia WGS AF: 0.466 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		-0.0010
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12767760; hg19: chr10-99294797;