4-143123185-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000507826.1(USP38-DT):​n.354+61323A>G 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 0.658 in 152,012 control chromosomes in the GnomAD database, including 33,198 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 0.66 ( 33198 hom., cov: 32)

Consequence

USP38-DT
ENST00000507826.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.138
Variant links:
Genes affected
USP38-DT (HGNC:55554): (USP38 divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
USP38-DTENST00000507826.1 linkuse as main transcriptn.354+61323A>G intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.658
AC:
100014
AN:
151894
Hom.:
33179
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.595
Gnomad AMI
AF:
0.805
Gnomad AMR
AF:
0.677
Gnomad ASJ
AF:
0.645
Gnomad EAS
AF:
0.830
Gnomad SAS
AF:
0.608
Gnomad FIN
AF:
0.727
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.671
Gnomad OTH
AF:
0.659
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.658
AC:
100082
AN:
152012
Hom.:
33198
Cov.:
32
AF XY:
0.663
AC XY:
49278
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.595
Gnomad4 AMR
AF:
0.677
Gnomad4 ASJ
AF:
0.645
Gnomad4 EAS
AF:
0.831
Gnomad4 SAS
AF:
0.607
Gnomad4 FIN
AF:
0.727
Gnomad4 NFE
AF:
0.671
Gnomad4 OTH
AF:
0.660
Alfa
AF:
0.657
Hom.:
16509
Bravo
AF:
0.654
Asia WGS
AF:
0.682
AC:
2369
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
5.1
DANN
Benign
0.67

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4270544; hg19: chr4-144044338; API