4-143082006-T-G

Variant names:

• chr4-143082006-T-G
• rs7686660
• ENST00000507826.2:n.354+102502A>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.354+102502A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,654 control chromosomes in the GnomAD database, including 9,581 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 0.34 (9581 hom., cov: 31)
• Consequence: USP38-DT ENST00000507826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 41 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP38-DT	NR_185979.1	n.354+102502A>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.354+102502A>C		intron_variant	Intron 1 of 3	4
USP38-DT	ENST00000733058.1	n.500+29051A>C		intron_variant	Intron 2 of 2
USP38-DT	ENST00000733059.1	n.494-2996A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51487 AN: 151536 Hom.: 9562 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.340 AC: 51549 AN: 151654 Hom.: 9581 Cov.: 31 AF XY: 0.351 AC XY: 26015 AN XY: 74072

African (AFR) AF: 0.420 AC: 17369 AN: 41376

American (AMR) AF: 0.410 AC: 6233 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 890 AN: 3462

East Asian (EAS) AF: 0.733 AC: 3763 AN: 5134

South Asian (SAS) AF: 0.393 AC: 1888 AN: 4810

European-Finnish (FIN) AF: 0.336 AC: 3538 AN: 10522

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16905 AN: 67838

Other (OTH) AF: 0.320 AC: 672 AN: 2102

Alfa AF: 0.282 Hom.: 28758

Bravo AF: 0.351

Asia WGS AF: 0.498 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.54
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7686660; hg19: chr4-144003159;