chr19-55487144-T-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020378.4(NAT14):​c.*188T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 10

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 1495

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		-0.14

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;