3-22466612-C-T

Variant names:

• chr3-22466612-C-T
• rs1463234
• ENST00000782573.1:n.591-1141G>A

Variant summary

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

The ENST00000782573.1(ENSG00000301888):​n.591-1141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,890 control chromosomes in the GnomAD database, including 3,378 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 0.20 (3378 hom., cov: 32)
• Consequence: ENSG00000301888 ENST00000782573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 2 publications found

Genes affected

ENSG00000301888 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782573.1. 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
	ENSG00000301888	ENST00000782573.1		n.591-1141G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30881 AN: 151772 Hom.: 3378 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.203 AC: 30892 AN: 151890 Hom.: 3378 Cov.: 32 AF XY: 0.204 AC XY: 15118 AN XY: 74248

African (AFR) AF: 0.249 AC: 10308 AN: 41418

American (AMR) AF: 0.139 AC: 2127 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 678 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1880 AN: 5158

South Asian (SAS) AF: 0.131 AC: 630 AN: 4822

European-Finnish (FIN) AF: 0.207 AC: 2171 AN: 10510

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12436 AN: 67944

Other (OTH) AF: 0.205 AC: 433 AN: 2108

Alfa AF: 0.200 Hom.: 1156

Bravo AF: 0.202

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.81
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1463234; hg19: chr3-22508103;