10-103092902-A-AAACTT

Position:

• chr10-103092902-A-AAACTT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001351169.2(NT5C2):​c.1159+232_1159+236dupAAGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.31 (7387 hom., cov: 0)
• Consequence: NT5C2 NM_001351169.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.19

Genes affected

NT5C2 (HGNC:8022): (5'-nucleotidase, cytosolic II) This gene encodes a hydrolase that serves as an important role in cellular purine metabolism by acting primarily on inosine 5'-monophosphate and other purine nucleotides. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-103092902-A-AAACTT is Benign according to our data. Variant chr10-103092902-A-AAACTT is described in ClinVar as [Benign]. Clinvar id is 667740.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C2	NM_001351169.2	c.1159+232_1159+236dupAAGTT		intron_variant		ENST00000404739.8	NP_001338098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000404739.8	c.1159+232_1159+236dupAAGTT		intron_variant		1	NM_001351169.2	ENSP00000383960.3

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47206 AN: 151644 Hom.: 7382 Cov.: 0

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.311 AC: 47240 AN: 151764 Hom.: 7387 Cov.: 0 AF XY: 0.308 AC XY: 22860 AN XY: 74188

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.316

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3837340; hg19: chr10-104852659;