19-55487144-T-A

Variant names:

• chr19-55487144-T-A
• rs7478
• NM_020378.4:c.*188T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020378.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT14	NM_020378.4	MANE Select	c.*188T>A		3_prime_UTR	Exon 3 of 3	NP_065111.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT14	ENST00000205194.5	TSL:1 MANE Select	c.*188T>A		3_prime_UTR	Exon 3 of 3	ENSP00000205194.3
	NAT14	ENST00000592719.1	TSL:5	n.121T>A		non_coding_transcript_exon	Exon 3 of 3
	NAT14	ENST00000588985.1	TSL:5	c.439-134T>A		intron	N/A	ENSP00000471807.1

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

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

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

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: 88 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29173 AN: 67910

Other (OTH) AF: 0.336 AC: 708 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.73
PhyloP100		-0.14
Mutation Taster		=98/2	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: rs7478; hg19: chr19-55998511;