10-103175836-G-C

Position:

• chr10-103175836-G-C

Variant summary

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

The NM_001351169.2(NT5C2):​c.-24-854C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 168,044 control chromosomes in the GnomAD database, including 14,343 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 0.41 (12942 hom., cov: 32)
  • Exomes 𝑓: 0.41 (1401 hom.)
• Consequence: NT5C2 NM_001351169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

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]

MARCKSL1P1 (HGNC:45239): (MARCKS like 1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5C2	NM_001351169.2	c.-24-854C>G		intron_variant		ENST00000404739.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C2	ENST00000404739.8	c.-24-854C>G		intron_variant		1	NM_001351169.2	P1
MARCKSL1P1	ENST00000412473.1	n.283G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62176 AN: 151808 Hom.: 12930 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.418

GnomAD4 exome AF: 0.408 AC: 6578 AN: 16118 Hom.: 1401 Cov.: 0 AF XY: 0.413 AC XY: 3733 AN XY: 9048

Gnomad4 AFR exome AF: 0.379

Gnomad4 AMR exome AF: 0.389

Gnomad4 ASJ exome AF: 0.392

Gnomad4 EAS exome AF: 0.475

Gnomad4 SAS exome AF: 0.457

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.401

Gnomad4 OTH exome AF: 0.416

GnomAD4 genome AF: 0.410 AC: 62231 AN: 151926 Hom.: 12942 Cov.: 32 AF XY: 0.408 AC XY: 30299 AN XY: 74260

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.421

Alfa AF: 0.422 Hom.: 1704

Bravo AF: 0.411

Asia WGS AF: 0.464 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10786740; hg19: chr10-104935593;