1-39667123-T-G

Variant names:

• chr1-39667123-T-G
• rs873917
• NM_032526.3:c.136-887A>C

Variant summary

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

The NM_032526.3(NT5C1A):​c.136-887A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,216 control chromosomes in the GnomAD database, including 31,240 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 0.64 (31240 hom., cov: 28)
• Consequence: NT5C1A NM_032526.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 12 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5C1A	NM_032526.3	c.136-887A>C		intron_variant	Intron 1 of 5	ENST00000235628.2	NP_115915.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5C1A	ENST00000235628.2	c.136-887A>C		intron_variant	Intron 1 of 5	1	NM_032526.3	ENSP00000235628.1

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96533 AN: 151098 Hom.: 31230 Cov.: 28

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.639 AC: 96577 AN: 151216 Hom.: 31240 Cov.: 28 AF XY: 0.639 AC XY: 47144 AN XY: 73764

African (AFR) AF: 0.570 AC: 23398 AN: 41060

American (AMR) AF: 0.591 AC: 9000 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2309 AN: 3464

East Asian (EAS) AF: 0.485 AC: 2501 AN: 5154

South Asian (SAS) AF: 0.682 AC: 3270 AN: 4794

European-Finnish (FIN) AF: 0.698 AC: 7194 AN: 10302

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46749 AN: 67920

Other (OTH) AF: 0.651 AC: 1367 AN: 2100

Alfa AF: 0.664 Hom.: 80995

Bravo AF: 0.625

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.49
PhyloP100		0.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs873917; hg19: chr1-40132795;