chr3-72468889-A-G

Variant names:

• chr3-72468889-A-G
• rs9832314
• ENST00000810549.1:n.412+9764A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000810549.1(ENSG00000305353):​n.412+9764A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 152,306 control chromosomes in the GnomAD database, including 467 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 0.063 (467 hom., cov: 32)
• Consequence: ENSG00000305353 ENST00000810549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 4 publications found

Genes affected

ENSG00000305353 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810549.1. 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
	ENSG00000305353	ENST00000810549.1		n.412+9764A>G		intron	N/A
	ENSG00000305353	ENST00000810550.1		n.371+9764A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9652 AN: 152188 Hom.: 464 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0485

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0634 AC: 9662 AN: 152306 Hom.: 467 Cov.: 32 AF XY: 0.0688 AC XY: 5125 AN XY: 74466

African (AFR) AF: 0.0436 AC: 1814 AN: 41576

American (AMR) AF: 0.0604 AC: 924 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1053 AN: 5184

South Asian (SAS) AF: 0.142 AC: 686 AN: 4822

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10610

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0541 AC: 3679 AN: 68024

Other (OTH) AF: 0.0643 AC: 136 AN: 2116

Alfa AF: 0.0629 Hom.: 58

Bravo AF: 0.0567

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	16
DANN	Benign	0.81
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs9832314; hg19: chr3-72518040;