rs71237667

Variant names:

• chr8-12138743-G-A
• rs71237667
• NM_201402.3:c.18C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-12138743-G-A
• chr8-12138743-G-C
• chr8-12138743-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_201402.3(USP17L2):​c.18C>T​(p.Leu6Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0762 in 1,360,934 control chromosomes in the GnomAD database, including 11,565 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 0.062 (1268 hom., cov: 32)
  • Exomes 𝑓: 0.078 (10297 hom.)
• Consequence: USP17L2 NM_201402.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

Genes affected

USP17L2 (HGNC:34434): (ubiquitin specific peptidase 17 like family member 2) DUB3 is a member of the ubiquitin processing protease (UBP) subfamily of deubiquitinating enzymes. See USP1 (MIM 603478) for background information.[supplied by OMIM, Mar 2008]

FAM66D (HGNC:24159): (family with sequence similarity 66 member D)

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP7: Synonymous conserved (PhyloP=0.036 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP17L2	NM_201402.3	c.18C>T	p.Leu6Leu	synonymous_variant	Exon 1 of 1	ENST00000333796.4	NP_958804.2
FAM66D	NR_027425.1	n.609-6680G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP17L2	ENST00000333796.4	c.18C>T	p.Leu6Leu	synonymous_variant	Exon 1 of 1	6	NM_201402.3	ENSP00000333329.3

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 8675 AN: 138866 Hom.: 1267 Cov.: 32

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0480

Gnomad EAS AF: 0.000940

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.00719

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.0447

GnomAD3 exomes AF: 0.0621 AC: 11183 AN: 180120 Hom.: 1334 AF XY: 0.0612 AC XY: 6058 AN XY: 98922

Gnomad AFR exome AF: 0.0162

Gnomad AMR exome AF: 0.0330

Gnomad ASJ exome AF: 0.0473

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0138

Gnomad FIN exome AF: 0.116

Gnomad NFE exome AF: 0.0919

Gnomad OTH exome AF: 0.0616

GnomAD4 exome AF: 0.0778 AC: 95051 AN: 1221980 Hom.: 10297 Cov.: 31 AF XY: 0.0760 AC XY: 46763 AN XY: 614988

Gnomad4 AFR exome AF: 0.0130

Gnomad4 AMR exome AF: 0.0353

Gnomad4 ASJ exome AF: 0.0485

Gnomad4 EAS exome AF: 0.000120

Gnomad4 SAS exome AF: 0.0146

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.0888

Gnomad4 OTH exome AF: 0.0656

GnomAD4 genome AF: 0.0624 AC: 8676 AN: 138954 Hom.: 1268 Cov.: 32 AF XY: 0.0622 AC XY: 4190 AN XY: 67312

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0465

Gnomad4 ASJ AF: 0.0480

Gnomad4 EAS AF: 0.000943

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0922

Gnomad4 OTH AF: 0.0437

Alfa AF: 0.0434 Hom.: 151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.71

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: rs71237667; hg19: chr8-11996252; COSMIC: COSV61555853; COSMIC: COSV61555853;