NM_024954.5:c.70+15246C>T

Variant names:

• chr10-97514519-C-T
• rs10786353
• NM_024954.5:c.70+15246C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024954.5(UBTD1):​c.70+15246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,944 control chromosomes in the GnomAD database, including 21,804 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 0.52 (21804 hom., cov: 31)
• Consequence: UBTD1 NM_024954.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 7 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBTD1	NM_024954.5	MANE Select	c.70+15246C>T		intron	N/A	NP_079230.1	Q9HAC8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBTD1	ENST00000370664.4	TSL:1 MANE Select	c.70+15246C>T		intron	N/A	ENSP00000359698.3	Q9HAC8
	UBTD1	ENST00000958439.1		c.163+530C>T		intron	N/A	ENSP00000628498.1
	UBTD1	ENST00000923989.1		c.70+15246C>T		intron	N/A	ENSP00000594048.1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78749 AN: 151826 Hom.: 21801 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.518 AC: 78766 AN: 151944 Hom.: 21804 Cov.: 31 AF XY: 0.522 AC XY: 38789 AN XY: 74250

African (AFR) AF: 0.322 AC: 13334 AN: 41426

American (AMR) AF: 0.610 AC: 9307 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1982 AN: 3470

East Asian (EAS) AF: 0.861 AC: 4459 AN: 5178

South Asian (SAS) AF: 0.703 AC: 3382 AN: 4810

European-Finnish (FIN) AF: 0.530 AC: 5591 AN: 10542

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38776 AN: 67948

Other (OTH) AF: 0.547 AC: 1148 AN: 2098

Alfa AF: 0.566 Hom.: 24186

Bravo AF: 0.518

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.92
PhyloP100		-0.15
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: rs10786353; hg19: chr10-99274276;