6-29466637-G-A

Variant names:

• chr6-29466637-G-A
• rs4713226
• ENST00000457888.2:n.23-1682C>T

Variant summary

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

The ENST00000457888.2(UBDP1):​n.23-1682C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 152,148 control chromosomes in the GnomAD database, including 715 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 0.087 (715 hom., cov: 32)
• Consequence: UBDP1 ENST00000457888.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 18 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457888.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBDP1	ENST00000457888.2	TSL:6	n.23-1682C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13249 AN: 152030 Hom.: 709 Cov.: 32

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.0411

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.0872 AC: 13264 AN: 152148 Hom.: 715 Cov.: 32 AF XY: 0.0884 AC XY: 6578 AN XY: 74376

African (AFR) AF: 0.0324 AC: 1344 AN: 41520

American (AMR) AF: 0.148 AC: 2259 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0828 AC: 287 AN: 3468

East Asian (EAS) AF: 0.222 AC: 1151 AN: 5176

South Asian (SAS) AF: 0.0417 AC: 201 AN: 4818

European-Finnish (FIN) AF: 0.103 AC: 1091 AN: 10572

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6589 AN: 67992

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.0922 Hom.: 2022

Bravo AF: 0.0932

Asia WGS AF: 0.0960 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.29
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4713226; hg19: chr6-29434414; COSMIC: COSV65810764;