Variant chr4-67756760-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.13

Variant links:

Genes affected

UBA6-DT (HGNC:):

UBA6-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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/exons	MANE	Protein	UniProt
	use as main transcript	n.67756760G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
UBA6-DT	ENST00000500538.7 linkuse as main transcript	n.1987+1505G>A	intron_variant	1
UBA6-DT	ENST00000502758.1 linkuse as main transcript	n.483+1505G>A	intron_variant	4
UBA6-DT	ENST00000660972.1 linkuse as main transcript	n.1357+1505G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68202

AN:

151884

Hom.:

16733

Cov.:

show subpopulations

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.:

AF XY:

0.455

AC XY:

33821

AN XY:

74296

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over