ENST00000500538.7:n.1920+935T>C

Variant names:

• chr4-67733280-T-C
• rs1843593
• ENST00000500538.7:n.1920+935T>C

Variant summary

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

The ENST00000500538.7(UBA6-DT):​n.1920+935T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 22 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBA6-DT	ENST00000500538.7	TSL:1	n.1920+935T>C		intron	N/A
	UBA6-DT	ENST00000502758.1	TSL:4	n.202+935T>C		intron	N/A
	UBA6-DT	ENST00000656992.1		n.1296+935T>C		intron	N/A

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

African (AFR) AF: 0.0737 AC: 3061 AN: 41560

American (AMR) AF: 0.139 AC: 2119 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3468

East Asian (EAS) AF: 0.138 AC: 711 AN: 5164

South Asian (SAS) AF: 0.217 AC: 1046 AN: 4816

European-Finnish (FIN) AF: 0.128 AC: 1356 AN: 10600

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9738 AN: 68010

Other (OTH) AF: 0.140 AC: 296 AN: 2116

Alfa AF: 0.143 Hom.: 2744

Bravo AF: 0.122

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.9
DANN	Benign	0.79
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1843593;

hg19: chr4-68598998;