4-143050089-C-T

Variant summary

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

The ENST00000507826.1(USP38-DT):n.355-109844G>A variant causes a intron, non coding transcript 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 ENST00000507826.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP38-DT	ENST00000507826.1	n.355-109844G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.560

Alfa AF: 0.475 Hom.: 1488

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4266246; hg19: chr4-143971242;