rs1438405

Variant names:

• chr4-67992826-A-G
• rs1438405
• ENST00000500538.7:n.1988-69781A>G

Variant summary

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

The ENST00000500538.7(UBA6-DT):​n.1988-69781A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,086 control chromosomes in the GnomAD database, including 32,655 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 0.62 (32655 hom., cov: 32)
• Consequence: UBA6-DT ENST00000500538.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 3 publications found

Genes affected

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

TMPRSS11GP (HGNC:42983): (transmembrane serine protease 11G, pseudogene)

ENSG00000290400 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMPRSS11GP	NR_033737.2	n.308-981T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBA6-DT	ENST00000500538.7	n.1988-69781A>G		intron_variant	Intron 6 of 7	1
TMPRSS11GP	ENST00000431070.6	n.1043-981T>C		intron_variant	Intron 8 of 8	6
ENSG00000290400	ENST00000502496.1	n.356-981T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93598 AN: 151968 Hom.: 32651 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.616 AC: 93627 AN: 152086 Hom.: 32655 Cov.: 32 AF XY: 0.617 AC XY: 45859 AN XY: 74350

African (AFR) AF: 0.278 AC: 11527 AN: 41478

American (AMR) AF: 0.565 AC: 8625 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2241 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4301 AN: 5168

South Asian (SAS) AF: 0.725 AC: 3490 AN: 4816

European-Finnish (FIN) AF: 0.745 AC: 7893 AN: 10600

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53355 AN: 67976

Other (OTH) AF: 0.614 AC: 1296 AN: 2112

Alfa AF: 0.741 Hom.: 21625

Bravo AF: 0.585

Asia WGS AF: 0.735 AC: 2557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.34
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1438405; hg19: chr4-68858544;