1-39655194-C-T

Variant summary

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

The NM_032526.3(NT5C1A):c.*3927G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,188 control chromosomes in the GnomAD database, including 2,257 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 0.17 (2257 hom., cov: 32)
• Consequence: NT5C1A NM_032526.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

NT5C1A (HGNC:17819): (5'-nucleotidase, cytosolic IA) Cytosolic nucleotidases, such as NT5C1A, dephosphorylate nucleoside monophosphates (Hunsucker et al., 2001 [PubMed 11133996]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5C1A	NM_032526.3	c.*3927G>A		3_prime_UTR_variant	6/6	ENST00000235628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C1A	ENST00000235628.2	c.*3927G>A		3_prime_UTR_variant	6/6	1	NM_032526.3	P1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25341 AN: 152070 Hom.: 2255 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.167 AC: 25367 AN: 152188 Hom.: 2257 Cov.: 32 AF XY: 0.166 AC XY: 12362 AN XY: 74410

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.194

Alfa AF: 0.0686 Hom.: 73

Bravo AF: 0.175

Asia WGS AF: 0.277 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1180273; hg19: chr1-40120866;