10-97500220-T-G

Variant names:

• chr10-97500220-T-G
• rs7893335
• NM_024954.5:c.70+947T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024954.5(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 NM_024954.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599
• 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 -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.

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+947T>G		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+947T>G		intron	N/A	ENSP00000359698.3	Q9HAC8
	UBTD1	ENST00000958439.1		c.70+947T>G		intron	N/A	ENSP00000628498.1
	UBTD1	ENST00000923989.1		c.70+947T>G		intron	N/A	ENSP00000594048.1

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

African (AFR) AF: 0.206 AC: 8552 AN: 41494

American (AMR) AF: 0.231 AC: 3541 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3464

East Asian (EAS) AF: 0.503 AC: 2597 AN: 5164

South Asian (SAS) AF: 0.385 AC: 1849 AN: 4804

European-Finnish (FIN) AF: 0.166 AC: 1758 AN: 10566

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11006 AN: 67982

Other (OTH) AF: 0.192 AC: 405 AN: 2106

Alfa AF: 0.174 Hom.: 3957

Bravo AF: 0.205

Asia WGS AF: 0.428 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.90
PhyloP100		0.60
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: rs7893335; hg19: chr10-99259977;