chr4-67756760-G-A

Variant names:

• chr4-67756760-G-A
• rs3756159
• ENST00000500538.7:n.1987+1505G>A

Variant summary

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

The ENST00000500538.7(UBA6-DT):​n.1987+1505G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,002 control chromosomes in the GnomAD database, including 16,748 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 0.45 (16748 hom., cov: 31)
• Consequence: UBA6-DT ENST00000500538.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.552 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.1987+1505G>A		intron	N/A
	UBA6-DT	ENST00000502758.1	TSL:4	n.483+1505G>A		intron	N/A
	UBA6-DT	ENST00000660972.1		n.1357+1505G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68202 AN: 151884 Hom.: 16733 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.449 AC: 68240 AN: 152002 Hom.: 16748 Cov.: 31 AF XY: 0.455 AC XY: 33821 AN XY: 74296

African (AFR) AF: 0.236 AC: 9768 AN: 41464

American (AMR) AF: 0.550 AC: 8401 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1740 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2883 AN: 5150

South Asian (SAS) AF: 0.570 AC: 2745 AN: 4820

European-Finnish (FIN) AF: 0.539 AC: 5685 AN: 10538

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35634 AN: 67968

Other (OTH) AF: 0.457 AC: 962 AN: 2106

Alfa AF: 0.488 Hom.: 2850

Bravo AF: 0.435

Asia WGS AF: 0.590 AC: 2052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.70
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs3756159; hg19: chr4-68622478;