chr10-103241753-A-G

Variant names:

• chr10-103241753-A-G
• rs1891292
• ENST00000819995.1:n.206A>G

Variant summary

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

The ENST00000819995.1(ENSG00000306663):​n.206A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,870 control chromosomes in the GnomAD database, including 21,383 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 0.53 (21383 hom., cov: 31)
• Consequence: ENSG00000306663 ENST00000819995.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 13 publications found

Genes affected

ENSG00000306663 (HGNC:):

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]

NT5C2 Gene-Disease associations (from GenCC):

• hereditary spastic paraplegia 45

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819995.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306663	ENST00000819995.1		n.206A>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000306663	ENST00000819996.1		n.88A>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000306663	ENST00000819997.1		n.83A>G		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80183 AN: 151754 Hom.: 21357 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.528 AC: 80258 AN: 151870 Hom.: 21383 Cov.: 31 AF XY: 0.525 AC XY: 38980 AN XY: 74228

African (AFR) AF: 0.498 AC: 20596 AN: 41396

American (AMR) AF: 0.535 AC: 8172 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3468

East Asian (EAS) AF: 0.540 AC: 2785 AN: 5162

South Asian (SAS) AF: 0.366 AC: 1763 AN: 4812

European-Finnish (FIN) AF: 0.522 AC: 5487 AN: 10510

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37701 AN: 67942

Other (OTH) AF: 0.538 AC: 1135 AN: 2110

Alfa AF: 0.543 Hom.: 97458

Bravo AF: 0.535

Asia WGS AF: 0.455 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	15
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1891292; hg19: chr10-105001510;