chr3-53274451-A-G

Variant names:

• chr3-53274451-A-G
• rs9821134
• ENST00000790869.1:n.278+4271A>G

Variant summary

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

The ENST00000790869.1(ENSG00000302984):​n.278+4271A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,044 control chromosomes in the GnomAD database, including 4,668 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 0.23 (4668 hom., cov: 32)
• Consequence: ENSG00000302984 ENST00000790869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 2 publications found

Genes affected

ENSG00000302984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790869.1. 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
	ENSG00000302984	ENST00000790869.1		n.278+4271A>G		intron	N/A
	ENSG00000302984	ENST00000790870.1		n.158+4271A>G		intron	N/A
	ENSG00000302984	ENST00000790871.1		n.158+4271A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34398 AN: 151926 Hom.: 4657 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.226 AC: 34433 AN: 152044 Hom.: 4668 Cov.: 32 AF XY: 0.220 AC XY: 16382 AN XY: 74318

African (AFR) AF: 0.374 AC: 15485 AN: 41426

American (AMR) AF: 0.150 AC: 2287 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3470

East Asian (EAS) AF: 0.0617 AC: 319 AN: 5170

South Asian (SAS) AF: 0.178 AC: 860 AN: 4824

European-Finnish (FIN) AF: 0.171 AC: 1810 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12519 AN: 67974

Other (OTH) AF: 0.213 AC: 450 AN: 2110

Alfa AF: 0.217 Hom.: 471

Bravo AF: 0.232

Asia WGS AF: 0.143 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs9821134; hg19: chr3-53308467;