chr16-23104063-T-C

Position:

• chr16-23104063-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020718.4(USP31):​c.1089+1378A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,158 control chromosomes in the GnomAD database, including 6,122 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 0.27 (6122 hom., cov: 32)
• Consequence: USP31 NM_020718.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

Genes affected

USP31 (HGNC:20060): (ubiquitin specific peptidase 31) Enables thiol-dependent deubiquitinase. Involved in protein deubiquitination. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

USP31 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USP31	NM_020718.4	c.1089+1378A>G		intron_variant		ENST00000219689.12	NP_065769.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP31	ENST00000219689.12	c.1089+1378A>G		intron_variant		1	NM_020718.4	ENSP00000219689.7

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41530 AN: 152040 Hom.: 6110 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.273 AC: 41585 AN: 152158 Hom.: 6122 Cov.: 32 AF XY: 0.274 AC XY: 20359 AN XY: 74372

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.276

Alfa AF: 0.299 Hom.: 1191

Bravo AF: 0.271

Asia WGS AF: 0.274 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1858799; hg19: chr16-23115384;