Genetic Variant NAT14:c.*188T>A (chr19-55487144-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020378.4(NAT14):c.*188T>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 0.399 in 903,338 control chromosomes in the GnomAD database, including 75,522 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 0.33 ( 9278 hom., cov: 33)

Exomes 𝑓: 0.41 ( 66244 hom. )

Consequence

NAT14
NM_020378.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.137

Publications

16 publications found

Variant links:

Genes affected

NAT14 (HGNC:28918): (N-acetyltransferase 14 (putative)) Predicted to enable N-acetyltransferase activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

NAT14 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAT14	NM_020378.4 link	c.*188T>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000205194.5	NP_065111.1	Q8WUY8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
NAT14	ENST00000205194.5 link	c.*188T>A	3_prime_UTR_variant	Exon 3 of 3	1	NM_020378.4	ENSP00000205194.3	Q8WUY8
NAT14	ENST00000592719.1 link	n.121T>A	non_coding_transcript_exon_variant	Exon 3 of 3	5
NAT14	ENST00000588985.1 link	c.439-134T>A	intron_variant	Intron 1 of 1	5		ENSP00000471807.1	M0R1E3
NAT14	ENST00000587400.1 link	c.11-90T>A	intron_variant	Intron 2 of 2	5		ENSP00000472383.1	M0R284

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49409

AN:

151886

Hom.:

9262

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.264

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.328

GnomAD4 exome

AF:

0.414

AC:

310679

AN:

751334

Hom.:

66244

Cov.:

AF XY:

0.417

AC XY:

157333

AN XY:

377198

show subpopulations

African (AFR)

AF:

0.129

AC:

1924

AN:

14868

American (AMR)

AF:

0.321

AC:

4371

AN:

13620

Ashkenazi Jewish (ASJ)

AF:

0.335

AC:

4818

AN:

14372

East Asian (EAS)

AF:

0.263

AC:

6954

AN:

26418

South Asian (SAS)

AF:

0.504

AC:

24751

AN:

49100

European-Finnish (FIN)

AF:

0.368

AC:

10847

AN:

29466

Middle Eastern (MID)

AF:

0.322

AC:

809

AN:

2516

European-Non Finnish (NFE)

AF:

0.429

AC:

242868

AN:

565736

Other (OTH)

AF:

0.378

AC:

13337

AN:

35238

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

9553

19106

28658

38211

47764

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5990

11980

17970

23960

29950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.325

AC:

49448

AN:

152004

Hom.:

9278

Cov.:

AF XY:

0.323

AC XY:

24024

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.135

AC:

5617

AN:

41502

American (AMR)

AF:

0.325

AC:

4965

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.342

AC:

1186

AN:

3472

East Asian (EAS)

AF:

0.264

AC:

1365

AN:

5168

South Asian (SAS)

AF:

0.496

AC:

2390

AN:

4816

European-Finnish (FIN)

AF:

0.337

AC:

3552

AN:

10540

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.430

AC:

29173

AN:

67910

Other (OTH)

AF:

0.336

AC:

708

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1652

3304

4957

6609

8261

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.372

Hom.:

1495

Bravo

AF:

0.309

Asia WGS

AF:

0.401

AC:

1392

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.6

(source)

DANN

Benign

0.73

PhyloP100

-0.14

Mutation Taster

=98/2

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over