4-143117986-T-C

Variant names:

• chr4-143117986-T-C
• rs28459062
• ENST00000507826.2:n.354+66522A>G

Variant summary

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

The ENST00000507826.2(USP38-DT):​n.354+66522A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 151,832 control chromosomes in the GnomAD database, including 1,080 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 0.11 (1080 hom., cov: 31)
• Consequence: USP38-DT ENST00000507826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 3 publications found

Genes affected

USP38-DT (HGNC:55554): (USP38 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP38-DT	NR_185979.1	n.354+66522A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP38-DT	ENST00000507826.2	n.354+66522A>G		intron_variant	Intron 1 of 3	4
USP38-DT	ENST00000733058.1	n.374-6803A>G		intron_variant	Intron 1 of 2
USP38-DT	ENST00000733059.1	n.367-6803A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16044 AN: 151714 Hom.: 1081 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.0710

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.106 AC: 16056 AN: 151832 Hom.: 1080 Cov.: 31 AF XY: 0.103 AC XY: 7660 AN XY: 74210

African (AFR) AF: 0.187 AC: 7752 AN: 41362

American (AMR) AF: 0.0690 AC: 1049 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3464

East Asian (EAS) AF: 0.0118 AC: 61 AN: 5162

South Asian (SAS) AF: 0.0701 AC: 337 AN: 4808

European-Finnish (FIN) AF: 0.0710 AC: 749 AN: 10556

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0834 AC: 5671 AN: 67962

Other (OTH) AF: 0.0985 AC: 207 AN: 2102

Alfa AF: 0.0970 Hom.: 177

Bravo AF: 0.110

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs28459062; hg19: chr4-144039139;