3-128597592-A-G

Variant names:

• chr3-128597592-A-G
• rs4328821
• ENST00000818594.1:n.270-5185T>C

Variant summary

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

The ENST00000818594.1(ENSG00000306450):​n.270-5185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,234 control chromosomes in the GnomAD database, including 1,584 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 0.13 (1584 hom., cov: 32)
• Consequence: ENSG00000306450 ENST00000818594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 27 publications found

Genes affected

ENSG00000306450 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818594.1. 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
	ENSG00000306450	ENST00000818594.1		n.270-5185T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20359 AN: 152116 Hom.: 1585 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.134 AC: 20382 AN: 152234 Hom.: 1584 Cov.: 32 AF XY: 0.135 AC XY: 10034 AN XY: 74414

African (AFR) AF: 0.134 AC: 5563 AN: 41544

American (AMR) AF: 0.166 AC: 2538 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3468

East Asian (EAS) AF: 0.353 AC: 1825 AN: 5176

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4816

European-Finnish (FIN) AF: 0.0812 AC: 861 AN: 10606

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7584 AN: 68016

Other (OTH) AF: 0.132 AC: 280 AN: 2114

Alfa AF: 0.125 Hom.: 4234

Bravo AF: 0.143

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.79
PhyloP100		-0.20

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: rs4328821;

hg19: chr3-128316435;