rs7478

chr19-55487144-T-Achr19-55487144-T-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NAT14	NM_020378.4	c.*188T>A		3_prime_UTR_variant	3/3	ENST00000205194.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAT14	ENST00000205194.5	c.*188T>A		3_prime_UTR_variant	3/3	1	NM_020378.4	P1
NAT14	ENST00000587400.1	c.11-90T>A		intron_variant		5
NAT14	ENST00000588985.1	c.440-134T>A		intron_variant		5
NAT14	ENST00000592719.1	n.121T>A		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49409 AN: 151886 Hom.: 9262 Cov.: 33

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.: 10 AF XY: 0.417 AC XY: 157333 AN XY: 377198

Gnomad4 AFR exome AF: 0.129

Gnomad4 AMR exome AF: 0.321

Gnomad4 ASJ exome AF: 0.335

Gnomad4 EAS exome AF: 0.263

Gnomad4 SAS exome AF: 0.504

Gnomad4 FIN exome AF: 0.368

Gnomad4 NFE exome AF: 0.429

Gnomad4 OTH exome AF: 0.378

GnomAD4 genome AF: 0.325 AC: 49448 AN: 152004 Hom.: 9278 Cov.: 33 AF XY: 0.323 AC XY: 24024 AN XY: 74286

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.336

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
Dann	Benign	0.73

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: rs7478; hg19: chr19-55998511;