rs3756159

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-67756760-G-A
• chr4-67756760-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.552 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.1987+1505G>A		intron_variant	Intron 6 of 7	1
UBA6-DT	ENST00000502758.1	n.483+1505G>A		intron_variant	Intron 5 of 5	4
UBA6-DT	ENST00000660972.1	n.1357+1505G>A		intron_variant	Intron 6 of 6

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

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.457

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756159; hg19: chr4-68622478;