chr4-67756817-G-A

Position:

• chr4-67756817-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.332 in 151,998 control chromosomes in the GnomAD database, including 8,599 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 0.33 (8599 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

Genes affected

UBA6-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67756817G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBA6-DT	ENST00000500538.7	n.1987+1562G>A		intron_variant		1
UBA6-DT	ENST00000502758.1	n.483+1562G>A		intron_variant		4
UBA6-DT	ENST00000660972.1	n.1357+1562G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50433 AN: 151880 Hom.: 8594 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.332 AC: 50444 AN: 151998 Hom.: 8599 Cov.: 31 AF XY: 0.333 AC XY: 24732 AN XY: 74290

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.349

Alfa AF: 0.326 Hom.: 1317

Bravo AF: 0.323

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12644822; hg19: chr4-68622535;