dbSNP rs13137565: USP38-DT:n.285C>T (chr4-143184545-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000507486.1(USP38-DT):n.285C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,254 control chromosomes in the GnomAD database, including 40,308 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 0.72 ( 40300 hom., cov: 35)

Exomes 𝑓: 0.73 ( 8 hom. )

Consequence

USP38-DT
ENST00000507486.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.263

Publications

5 publications found

Variant links:

Genes affected

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

USP38-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP38-DT	NR_136203.2 link	n.317C>T		non_coding_transcript_exon_variant	Exon 1 of 2
USP38-DT	NR_185979.1 link	n.317C>T		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
USP38-DT	ENST00000507486.1 link	n.285C>T	non_coding_transcript_exon_variant	Exon 1 of 2	3
USP38-DT	ENST00000507826.2 link	n.317C>T	non_coding_transcript_exon_variant	Exon 1 of 4	4
USP38-DT	ENST00000657857.2 link	n.360C>T	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.723

AC:

110042

AN:

152106

Hom.:

40251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.827

Gnomad AMI

AF:

0.788

Gnomad AMR

AF:

0.699

Gnomad ASJ

AF:

0.629

Gnomad EAS

AF:

0.829

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.727

Gnomad MID

AF:

0.668

Gnomad NFE

AF:

0.672

Gnomad OTH

AF:

0.707

GnomAD4 exome

AF:

0.733

AC:

AN:

Hom.:

Cov.:

AF XY:

0.727

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.786

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.533

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.724

AC:

110152

AN:

152224

Hom.:

40300

Cov.:

AF XY:

0.725

AC XY:

53925

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.827

AC:

34372

AN:

41566

American (AMR)

AF:

0.699

AC:

10691

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.629

AC:

2181

AN:

3470

East Asian (EAS)

AF:

0.830

AC:

4281

AN:

5158

South Asian (SAS)

AF:

0.589

AC:

2842

AN:

4824

European-Finnish (FIN)

AF:

0.727

AC:

7710

AN:

10608

Middle Eastern (MID)

AF:

0.660

AC:

194

AN:

294

European-Non Finnish (NFE)

AF:

0.672

AC:

45674

AN:

67992

Other (OTH)

AF:

0.707

AC:

1490

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1544

3087

4631

6174

7718

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

840

1680

2520

3360

4200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.681

Hom.:

16153

Bravo

AF:

0.730

Asia WGS

AF:

0.689

AC:

2396

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.3

(source)

DANN

Benign

0.85

PhyloP100

0.26

PromoterAI

-0.0094

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over