1-39659439-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Moderate BP6_Moderate BP7

The NM_032526.3(NT5C1A):c.789G>A(p.Lys263=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00282 in 1,606,210 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0021 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0029 (3 hom.)
• Consequence: NT5C1A NM_032526.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.02

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 Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BP6: Variant 1-39659439-C-T is Benign according to our data. Variant chr1-39659439-C-T is described in ClinVar as [Benign]. Clinvar id is 711052.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=1.02 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5C1A	NM_032526.3	c.789G>A	p.Lys263=	synonymous_variant	6/6	ENST00000235628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C1A	ENST00000235628.2	c.789G>A	p.Lys263=	synonymous_variant	6/6	1	NM_032526.3	P1

Frequencies

GnomAD3 genomes AF: 0.00209 AC: 318 AN: 152262 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000720

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00452

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00354

Gnomad OTH AF: 0.000955

GnomAD3 exomes AF: 0.00217 AC: 536 AN: 247076 Hom.: 0 AF XY: 0.00213 AC XY: 285 AN XY: 133544

Gnomad AFR exome AF: 0.000619

Gnomad AMR exome AF: 0.000414

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00461

Gnomad NFE exome AF: 0.00362

Gnomad OTH exome AF: 0.00133

GnomAD4 exome AF: 0.00289 AC: 4206 AN: 1453830 Hom.: 3 Cov.: 31 AF XY: 0.00275 AC XY: 1984 AN XY: 721938

Gnomad4 AFR exome AF: 0.000421

Gnomad4 AMR exome AF: 0.000498

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000585

Gnomad4 FIN exome AF: 0.00521

Gnomad4 NFE exome AF: 0.00340

Gnomad4 OTH exome AF: 0.00198

GnomAD4 genome AF: 0.00209 AC: 318 AN: 152380 Hom.: 0 Cov.: 33 AF XY: 0.00207 AC XY: 154 AN XY: 74524

Gnomad4 AFR AF: 0.000361

Gnomad4 AMR AF: 0.000719

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00452

Gnomad4 NFE AF: 0.00354

Gnomad4 OTH AF: 0.000945

Alfa AF: 0.00305 Hom.: 0

Bravo AF: 0.00172

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jul 26, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
Cadd	Benign	7.6
Dann	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs139206635; hg19: chr1-40125111;