ENST00000457888.2:n.23-1563G>A

Variant names:

• chr6-29466518-C-T
• rs2107191
• ENST00000457888.2:n.23-1563G>A

Variant summary

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

The ENST00000457888.2(UBDP1):​n.23-1563G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,028 control chromosomes in the GnomAD database, including 30,658 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 0.63 (30658 hom., cov: 32)
• Consequence: UBDP1 ENST00000457888.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 21 publications found

Genes affected

UBDP1 (HGNC:18796): (ubiquitin D pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBDP1	ENST00000457888.2	n.23-1563G>A		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95370 AN: 151910 Hom.: 30605 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.628 AC: 95481 AN: 152028 Hom.: 30658 Cov.: 32 AF XY: 0.628 AC XY: 46622 AN XY: 74286

African (AFR) AF: 0.771 AC: 31985 AN: 41492

American (AMR) AF: 0.554 AC: 8461 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1626 AN: 3466

East Asian (EAS) AF: 0.590 AC: 3046 AN: 5164

South Asian (SAS) AF: 0.649 AC: 3127 AN: 4816

European-Finnish (FIN) AF: 0.623 AC: 6570 AN: 10540

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38748 AN: 67970

Other (OTH) AF: 0.616 AC: 1299 AN: 2108

Alfa AF: 0.583 Hom.: 60761

Bravo AF: 0.630

Asia WGS AF: 0.653 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2107191; hg19: chr6-29434295;