rs1843593

Positions:

• chr4-67733280-T-C

Variant summary

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

The ENST00000500538.7(UBA6-DT):​n.1920+935T>C 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 0.126 in 152,234 control chromosomes in the GnomAD database, including 1,346 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 0.13 (1346 hom., cov: 32)
• Consequence: UBA6-DT ENST00000500538.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBA6-DT	ENST00000500538.7	n.1920+935T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19197 AN: 152116 Hom.: 1343 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.126 AC: 19210 AN: 152234 Hom.: 1346 Cov.: 32 AF XY: 0.126 AC XY: 9415 AN XY: 74428

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.140

Alfa AF: 0.146 Hom.: 2285

Bravo AF: 0.122

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1843593; hg19: chr4-68598998;