chr2-73642883-C-T

Variant names:

• chr2-73642883-C-T
• rs4852954
• ENST00000852385.1:c.-84G>A

Variant summary

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

The ENST00000852385.1(NAT8):​c.-84G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,844 control chromosomes in the GnomAD database, including 23,073 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 0.52 (23073 hom., cov: 31)
• Consequence: NAT8 ENST00000852385.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000852385.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAT8	ENST00000852385.1		c.-84G>A		5_prime_UTR	Exon 1 of 2	ENSP00000522444.1
	NAT8	ENST00000852386.1		c.-849G>A		5_prime_UTR	Exon 1 of 2	ENSP00000522445.1
	NAT8	ENST00000852387.1		c.-202G>A		5_prime_UTR	Exon 1 of 2	ENSP00000522446.1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79283 AN: 151728 Hom.: 23074 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.522 AC: 79295 AN: 151844 Hom.: 23073 Cov.: 31 AF XY: 0.530 AC XY: 39297 AN XY: 74214

African (AFR) AF: 0.244 AC: 10088 AN: 41418

American (AMR) AF: 0.634 AC: 9626 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3468

East Asian (EAS) AF: 0.672 AC: 3463 AN: 5150

South Asian (SAS) AF: 0.675 AC: 3243 AN: 4802

European-Finnish (FIN) AF: 0.640 AC: 6760 AN: 10558

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42001 AN: 67942

Other (OTH) AF: 0.554 AC: 1167 AN: 2108

Alfa AF: 0.570 Hom.: 36453

Bravo AF: 0.510

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
DANN	Benign	0.48
PhyloP100		-0.58
PromoterAI		-0.060	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4852954;

hg19: chr2-73870010;