rs2630488

Variant names:

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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBA6-DT	ENST00000500538.7	n.984-424A>G		intron_variant	Intron 3 of 7	1
UBA6-DT	ENST00000656992.1	n.360-424A>G		intron_variant	Intron 2 of 4
UBA6-DT	ENST00000660972.1	n.272-424A>G		intron_variant	Intron 2 of 6

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;