10-103175836-G-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001351169.2(NT5C2):​c.-24-854C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

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>T		intron	N/A	NP_001338098.1
	NT5C2	NM_001351170.2		c.-24-854C>T		intron	N/A	NP_001338099.1
	NT5C2	NM_001351171.2		c.-24-854C>T		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>T		intron	N/A	ENSP00000383960.3
	NT5C2	ENST00000343289.9	TSL:1	c.-24-854C>T		intron	N/A	ENSP00000339479.5
	MARCKSL1P1	ENST00000412473.1	TSL:6	n.283G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 16220 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 9104

African (AFR) AF: 0.00 AC: 0 AN: 290

American (AMR) AF: 0.00 AC: 0 AN: 714

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 284

East Asian (EAS) AF: 0.00 AC: 0 AN: 1144

South Asian (SAS) AF: 0.00 AC: 0 AN: 1474

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 892

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 178

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 10374

Other (OTH) AF: 0.00 AC: 0 AN: 870

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.5
DANN	Benign	0.69
PhyloP100		-0.084

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;