10-103175836-G-C

Variant names:

• chr10-103175836-G-C
• rs10786740
• NM_001351169.2:c.-24-854C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351169.2. 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
	NT5C2	NM_001351169.2	MANE Select	c.-24-854C>G		intron	N/A	NP_001338098.1
	NT5C2	NM_001351170.2		c.-24-854C>G		intron	N/A	NP_001338099.1
	NT5C2	NM_001351171.2		c.-24-854C>G		intron	N/A	NP_001338100.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5C2	ENST00000404739.8	TSL:1 MANE Select	c.-24-854C>G		intron	N/A	ENSP00000383960.3
	NT5C2	ENST00000343289.9	TSL:1	c.-24-854C>G		intron	N/A	ENSP00000339479.5
	MARCKSL1P1	ENST00000412473.1	TSL:6	n.283G>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.379 AC: 110 AN: 290

American (AMR) AF: 0.389 AC: 276 AN: 710

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 109 AN: 278

East Asian (EAS) AF: 0.475 AC: 542 AN: 1142

South Asian (SAS) AF: 0.457 AC: 669 AN: 1464

European-Finnish (FIN) AF: 0.333 AC: 295 AN: 886

Middle Eastern (MID) AF: 0.449 AC: 80 AN: 178

European-Non Finnish (NFE) AF: 0.401 AC: 4137 AN: 10304

Other (OTH) AF: 0.416 AC: 360 AN: 866

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

African (AFR) AF: 0.389 AC: 16109 AN: 41428

American (AMR) AF: 0.403 AC: 6144 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1506 AN: 3466

East Asian (EAS) AF: 0.550 AC: 2833 AN: 5150

South Asian (SAS) AF: 0.449 AC: 2164 AN: 4820

European-Finnish (FIN) AF: 0.368 AC: 3890 AN: 10568

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

European-Non Finnish (NFE) AF: 0.416 AC: 28252 AN: 67924

Other (OTH) AF: 0.421 AC: 887 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.1
DANN	Benign	0.76
PhyloP100		-0.084
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10786740; hg19: chr10-104935593;