chr4-143022059-A-G

Variant names:

• chr4-143022059-A-G
• rs17017180
• ENST00000507826.2:n.355-81814T>C

Variant summary

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

The ENST00000507826.2(USP38-DT):​n.355-81814T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,942 control chromosomes in the GnomAD database, including 24,839 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 0.56 (24839 hom., cov: 32)
• Consequence: USP38-DT ENST00000507826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP38-DT	NR_185979.1	n.355-81814T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP38-DT	ENST00000507826.2	n.355-81814T>C		intron_variant	Intron 1 of 3	4
USP38-DT	ENST00000733058.1	n.501-8970T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85015 AN: 151824 Hom.: 24831 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.560 AC: 85064 AN: 151942 Hom.: 24839 Cov.: 32 AF XY: 0.550 AC XY: 40847 AN XY: 74238

African (AFR) AF: 0.421 AC: 17418 AN: 41414

American (AMR) AF: 0.514 AC: 7851 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2370 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5160

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4818

European-Finnish (FIN) AF: 0.580 AC: 6118 AN: 10546

Middle Eastern (MID) AF: 0.607 AC: 176 AN: 290

European-Non Finnish (NFE) AF: 0.667 AC: 45342 AN: 67952

Other (OTH) AF: 0.580 AC: 1224 AN: 2112

Alfa AF: 0.607 Hom.: 3914

Bravo AF: 0.545

Asia WGS AF: 0.433 AC: 1502 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.66
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs17017180; hg19: chr4-143943212;