chr2-73642781-G-A

Variant names:

• chr2-73642781-G-A
• rs4852953
• ENST00000852387.1:c.-100C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000852387.1(NAT8):​c.-100C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,442 control chromosomes in the GnomAD database, including 22,731 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 0.51 (22731 hom., cov: 31)
• Consequence: NAT8 ENST00000852387.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 2 publications found

Genes affected

NAT8 (HGNC:18069): (N-acetyltransferase 8 (putative)) This gene, isolated using the differential display method to detect tissue-specific genes, is specifically expressed in kidney and liver. The encoded protein shows amino acid sequence similarity to N-acetyltransferases. A similar protein in Xenopus affects cell adhesion and gastrulation movements, and may be localized in the secretory pathway. A highly similar paralog is found in a cluster with this gene. [provided by RefSeq, Sep 2008]

ALMS1P1 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000852387.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT8	ENST00000852387.1		c.-100C>T		5_prime_UTR	Exon 1 of 2	ENSP00000522446.1
	NAT8	ENST00000852385.1		c.-75+93C>T		intron	N/A	ENSP00000522444.1
	NAT8	ENST00000852386.1		c.-840+93C>T		intron	N/A	ENSP00000522445.1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77377 AN: 151324 Hom.: 22737 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.547

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.511 AC: 77373 AN: 151442 Hom.: 22731 Cov.: 31 AF XY: 0.517 AC XY: 38235 AN XY: 73940

African (AFR) AF: 0.197 AC: 8149 AN: 41426

American (AMR) AF: 0.551 AC: 8366 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2242 AN: 3446

East Asian (EAS) AF: 0.667 AC: 3398 AN: 5092

South Asian (SAS) AF: 0.682 AC: 3278 AN: 4808

European-Finnish (FIN) AF: 0.640 AC: 6711 AN: 10482

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.639 AC: 43271 AN: 67720

Other (OTH) AF: 0.548 AC: 1149 AN: 2098

Alfa AF: 0.568 Hom.: 3287

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.56
PhyloP100		1.1
PromoterAI		0.024	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4852953; hg19: chr2-73869908;