4-143050089-C-T

Variant names:

• chr4-143050089-C-T
• rs4266246
• ENST00000507826.2:n.355-109844G>A

Variant summary

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

The ENST00000507826.2(USP38-DT):​n.355-109844G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,900 control chromosomes in the GnomAD database, including 23,044 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 0.53 (23044 hom., cov: 32)
• Consequence: USP38-DT ENST00000507826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• 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=-0.9).
• 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.355-109844G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP38-DT	ENST00000507826.2	n.355-109844G>A		intron_variant	Intron 1 of 3	4
USP38-DT	ENST00000733058.1	n.501-37000G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80024 AN: 151782 Hom.: 23043 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.527 AC: 80057 AN: 151900 Hom.: 23044 Cov.: 32 AF XY: 0.519 AC XY: 38549 AN XY: 74220

African (AFR) AF: 0.304 AC: 12582 AN: 41384

American (AMR) AF: 0.506 AC: 7712 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2367 AN: 3472

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5164

South Asian (SAS) AF: 0.540 AC: 2600 AN: 4814

European-Finnish (FIN) AF: 0.581 AC: 6117 AN: 10532

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45346 AN: 67968

Other (OTH) AF: 0.560 AC: 1180 AN: 2108

Alfa AF: 0.460 Hom.: 1525

Bravo AF: 0.508

Asia WGS AF: 0.430 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.61
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4266246; hg19: chr4-143971242;