rs10498059

Variant names:

• chr2-218477182-T-C
• rs10498059
• NM_020935.3:c.1902-201A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-218477182-T-C
• chr2-218477182-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020935.3(USP37):​c.1902-201A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,350 control chromosomes in the GnomAD database, including 119 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 0.034 (119 hom., cov: 33)
• Consequence: USP37 NM_020935.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 2 publications found

Genes affected

USP37 (HGNC:20063): (ubiquitin specific peptidase 37) Enables cysteine-type endopeptidase activity; protein kinase binding activity; and thiol-dependent deubiquitinase. Involved in G1/S transition of mitotic cell cycle; protein deubiquitination; and regulation of DNA replication. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020935.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP37	NM_020935.3	MANE Select	c.1902-201A>G		intron	N/A	NP_065986.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP37	ENST00000258399.8	TSL:1 MANE Select	c.1902-201A>G		intron	N/A	ENSP00000258399.3
	USP37	ENST00000418019.5	TSL:1	c.1902-201A>G		intron	N/A	ENSP00000396585.1
	USP37	ENST00000415516.5	TSL:1	c.1620-201A>G		intron	N/A	ENSP00000400902.1

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 5200 AN: 152232 Hom.: 118 Cov.: 33

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0342 AC: 5205 AN: 152350 Hom.: 119 Cov.: 33 AF XY: 0.0338 AC XY: 2522 AN XY: 74508

African (AFR) AF: 0.0316 AC: 1314 AN: 41582

American (AMR) AF: 0.0203 AC: 310 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3472

East Asian (EAS) AF: 0.118 AC: 610 AN: 5190

South Asian (SAS) AF: 0.0443 AC: 214 AN: 4828

European-Finnish (FIN) AF: 0.0270 AC: 287 AN: 10624

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0332 AC: 2261 AN: 68030

Other (OTH) AF: 0.0326 AC: 69 AN: 2116

Alfa AF: 0.0270 Hom.: 41

Bravo AF: 0.0338

Asia WGS AF: 0.0690 AC: 239 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.76
DANN	Benign	0.73
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10498059; hg19: chr2-219341905;