Variant rs1041983 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000015.3(NAT2):c.282C>T(p.Tyr94=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151710 control chromosomes in the gnomAD Genomes database, including 10194 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 0.36 ( 10194 hom., cov: 31)

Exomes 𝑓: 0.34 ( 15264 hom. )

Consequence

NAT2
NM_000015.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750

Links

NAT2 (HGNC:7646):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP7

Synonymous conserved (PhyloP=-0.075 with no splicing effect.

BA1

GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAT2	NM_000015.3 linkuse as main transcript	c.282C>T	p.Tyr94=	synonymous_variant	2/2	ENST00000286479.4
NAT2	XM_017012938.2 linkuse as main transcript	c.282C>T	p.Tyr94=	synonymous_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAT2	ENST00000286479.4 linkuse as main transcript	c.282C>T	p.Tyr94=	synonymous_variant	2/2	1	NM_000015.3	P1
NAT2	ENST00000520116.1 linkuse as main transcript	c.-57-52C>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54604

AN:

151710

Hom.:

10194

Cov.:

show subpopulations

Gnomad AFR

AF:

0.450

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.321

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.412

Gnomad SAS

AF:

0.439

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.334

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.362

GnomAD3 exomes

AF:

0.342

AC:

85599

AN:

250306

Hom.:

15264

AF XY:

0.344

AC XY:

46546

AN XY:

135260

show subpopulations

Gnomad AFR exome

AF:

0.449

Gnomad AMR exome

AF:

0.304

Gnomad ASJ exome

AF:

0.372

Gnomad EAS exome

AF:

0.419

Gnomad SAS exome

AF:

0.428

Gnomad FIN exome

AF:

0.274

Gnomad NFE exome

AF:

0.313

Gnomad OTH exome

AF:

0.330

GnomAD4 exome

AF:

0.328

AC:

479746

AN:

1460778

Hom.:

80426

AF XY:

0.331

AC XY:

240168

AN XY:

726604

show subpopulations

Gnomad4 AFR exome

AF:

0.455

Gnomad4 AMR exome

AF:

0.307

Gnomad4 ASJ exome

AF:

0.382

Gnomad4 EAS exome

AF:

0.352

Gnomad4 SAS exome

AF:

0.428

Gnomad4 FIN exome

AF:

0.278

Gnomad4 NFE exome

AF:

0.317

Gnomad4 OTH exome

AF:

0.347

Alfa

AF:

0.327

Hom.:

17518

Bravo

AF:

0.363

Asia WGS

AF:

0.432

AC:

1503

AN:

3478

EpiCase

AF:

0.319

EpiControl

AF:

0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

Cadd

Benign

0.77

Dann

Benign

0.28

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over