Genetic Variant ENST00000755297.1:n.32+4464C>T (chr6-31275570-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000755297.1(ENSG00000298396):n.32+4464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 339,942 control chromosomes in the GnomAD database, including 6,849 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 0.19 ( 2970 hom., cov: 33)

Exomes 𝑓: 0.19 ( 3879 hom. )

Consequence

ENSG00000298396
ENST00000755297.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.474

Publications

24 publications found

Variant links:

Genes affected

ENSG00000298396 (HGNC:):

ENSG00000298396 links:

USP8P1 (HGNC:13987): (USP8 pseudogene 1)

USP8P1 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=-0.64).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1 link	n.32+4464C>T		intron_variant	Intron 1 of 1
USP8P1	ENST00000494673.1 link	n.-2C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29611

AN:

151882

Hom.:

2967

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.0847

Gnomad EAS

AF:

0.299

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.164

GnomAD4 exome

AF:

0.187

AC:

35089

AN:

187942

Hom.:

3879

Cov.:

AF XY:

0.183

AC XY:

18723

AN XY:

102222

show subpopulations

African (AFR)

AF:

0.167

AC:

679

AN:

4068

American (AMR)

AF:

0.136

AC:

1162

AN:

8560

Ashkenazi Jewish (ASJ)

AF:

0.0915

AC:

388

AN:

4240

East Asian (EAS)

AF:

0.231

AC:

2501

AN:

10836

South Asian (SAS)

AF:

0.198

AC:

5019

AN:

25370

European-Finnish (FIN)

AF:

0.254

AC:

4174

AN:

16418

Middle Eastern (MID)

AF:

0.175

AC:

123

AN:

704

European-Non Finnish (NFE)

AF:

0.179

AC:

19288

AN:

107978

Other (OTH)

AF:

0.180

AC:

1755

AN:

9768

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1220

2441

3661

4882

6102

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

134

268

402

536

670

<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:

0.195

AC:

29621

AN:

152000

Hom.:

2970

Cov.:

AF XY:

0.199

AC XY:

14761

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.189

AC:

7855

AN:

41458

American (AMR)

AF:

0.197

AC:

3009

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0847

AC:

294

AN:

3470

East Asian (EAS)

AF:

0.299

AC:

1549

AN:

5174

South Asian (SAS)

AF:

0.201

AC:

968

AN:

4826

European-Finnish (FIN)

AF:

0.261

AC:

2752

AN:

10528

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.187

AC:

12703

AN:

67946

Other (OTH)

AF:

0.164

AC:

346

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1243

2486

3730

4973

6216

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

336

672

1008

1344

1680

<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:

0.192

Hom.:

5723

Bravo

AF:

0.189

Asia WGS

AF:

0.274

AC:

951

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

5.9

(source)

DANN

Benign

0.62

PhyloP100

0.47

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