chr10-97514519-C-T

Position:

• chr10-97514519-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBTD1	NM_024954.5	c.70+15246C>T		intron_variant		ENST00000370664.4	NP_079230.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBTD1	ENST00000370664.4	c.70+15246C>T		intron_variant		1	NM_024954.5	ENSP00000359698.3

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

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.547

Alfa AF: 0.577 Hom.: 19233

Bravo AF: 0.518

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.92

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: rs10786353; hg19: chr10-99274276;