4-143152759-A-G

Variant names:

• chr4-143152759-A-G
• rs11100775
• ENST00000507826.2:n.354+31749T>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+31749T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,732 control chromosomes in the GnomAD database, including 6,262 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 0.28 (6262 hom., cov: 31)
• Consequence: USP38-DT ENST00000507826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP38-DT	NR_185979.1	n.354+31749T>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+31749T>C		intron_variant	Intron 1 of 3	4
USP38-DT	ENST00000733058.1	n.373+31749T>C		intron_variant	Intron 1 of 2
USP38-DT	ENST00000733059.1	n.366+31749T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42037 AN: 151614 Hom.: 6263 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.277 AC: 42049 AN: 151732 Hom.: 6262 Cov.: 31 AF XY: 0.276 AC XY: 20478 AN XY: 74184

African (AFR) AF: 0.173 AC: 7180 AN: 41432

American (AMR) AF: 0.302 AC: 4601 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1289 AN: 3470

East Asian (EAS) AF: 0.171 AC: 885 AN: 5172

South Asian (SAS) AF: 0.411 AC: 1977 AN: 4814

European-Finnish (FIN) AF: 0.273 AC: 2847 AN: 10418

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22355 AN: 67880

Other (OTH) AF: 0.295 AC: 621 AN: 2106

Alfa AF: 0.320 Hom.: 8438

Bravo AF: 0.270

Asia WGS AF: 0.311 AC: 1080 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.75
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs11100775; hg19: chr4-144073912;