4-67729650-A-G

Variant names:

• chr4-67729650-A-G
• rs2630488
• ENST00000500538.7:n.984-424A>G

Variant summary

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

The ENST00000500538.7(UBA6-DT):​n.984-424A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,956 control chromosomes in the GnomAD database, including 20,067 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 0.51 (20067 hom., cov: 32)
• Consequence: UBA6-DT ENST00000500538.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 6 publications found

Genes affected

UBA6-DT (HGNC:49083): (UBA6 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500538.7. 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
	UBA6-DT	ENST00000500538.7	TSL:1	n.984-424A>G		intron	N/A
	UBA6-DT	ENST00000656992.1		n.360-424A>G		intron	N/A
	UBA6-DT	ENST00000660972.1		n.272-424A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76847 AN: 151836 Hom.: 20040 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.506 AC: 76917 AN: 151956 Hom.: 20067 Cov.: 32 AF XY: 0.502 AC XY: 37267 AN XY: 74262

African (AFR) AF: 0.621 AC: 25732 AN: 41434

American (AMR) AF: 0.468 AC: 7143 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1710 AN: 5172

South Asian (SAS) AF: 0.368 AC: 1774 AN: 4826

European-Finnish (FIN) AF: 0.484 AC: 5104 AN: 10546

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31828 AN: 67926

Other (OTH) AF: 0.495 AC: 1046 AN: 2112

Alfa AF: 0.483 Hom.: 3206

Bravo AF: 0.516

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.58
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2630488; hg19: chr4-68595368;