rs2630488

chr4-67729650-A-G

Variant summary

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

The ENST00000500538.7(UBA6-DT):n.984-424A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBA6-DT	ENST00000500538.7	n.984-424A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.495

Alfa AF: 0.480 Hom.: 3066

Bravo AF: 0.516

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.68
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2630488; hg19: chr4-68595368;