rs13138607

Variant names:

• chr4-67755832-G-A
• rs13138607
• ENST00000500538.7:n.1987+577G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-67755832-G-A
• chr4-67755832-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000500538.7(UBA6-DT):​n.1987+577G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,746 control chromosomes in the GnomAD database, including 16,633 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.45 (16633 hom., cov: 32)
• Consequence: UBA6-DT ENST00000500538.7 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.365
• Publications: 10 publications found

Genes affected

UBA6-DT (HGNC:49083): (UBA6 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 4-67755832-G-A is Benign according to our data. Variant chr4-67755832-G-A is described in ClinVar as Benign. ClinVar VariationId is 349482.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.553 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+577G>A		intron_variant	Intron 6 of 7	1
UBA6-DT	ENST00000502758.1	n.483+577G>A		intron_variant	Intron 5 of 5	4
UBA6-DT	ENST00000660972.1	n.1357+577G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67870 AN: 151632 Hom.: 16617 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.448 AC: 67909 AN: 151746 Hom.: 16633 Cov.: 32 AF XY: 0.454 AC XY: 33654 AN XY: 74136

African (AFR) AF: 0.231 AC: 9537 AN: 41324

American (AMR) AF: 0.549 AC: 8385 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1740 AN: 3464

East Asian (EAS) AF: 0.560 AC: 2884 AN: 5146

South Asian (SAS) AF: 0.570 AC: 2753 AN: 4826

European-Finnish (FIN) AF: 0.541 AC: 5674 AN: 10482

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.523 AC: 35555 AN: 67924

Other (OTH) AF: 0.455 AC: 959 AN: 2110

Alfa AF: 0.485 Hom.: 15533

Bravo AF: 0.433

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypogonadotropic hypogonadism 7 with or without anosmia Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

Jun 26, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.45
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs13138607; hg19: chr4-68621550;