10-97500220-T-G

Position:

• chr10-97500220-T-G

Variant summary

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

The ENST00000370664.4(UBTD1):​c.70+947T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,082 control chromosomes in the GnomAD database, including 3,546 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 0.20 (3546 hom., cov: 32)
• Consequence: UBTD1 ENST00000370664.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599

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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBTD1	NM_024954.5	c.70+947T>G		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+947T>G		intron_variant		1	NM_024954.5	ENSP00000359698	P1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30910 AN: 151964 Hom.: 3536 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.203 AC: 30941 AN: 152082 Hom.: 3546 Cov.: 32 AF XY: 0.208 AC XY: 15483 AN XY: 74334

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.192

Alfa AF: 0.175 Hom.: 3362

Bravo AF: 0.205

Asia WGS AF: 0.428 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.90

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: rs7893335; hg19: chr10-99259977;