3-99333303-A-G

Variant names:

• chr3-99333303-A-G
• rs9861463
• ENST00000715235.1:n.51+1851A>G

Variant summary

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

The ENST00000715235.1(ENSG00000243296):​n.51+1851A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 150,680 control chromosomes in the GnomAD database, including 22,820 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 0.50 (22820 hom., cov: 30)
• Consequence: ENSG00000243296 ENST00000715235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 4 publications found

Genes affected

ENSG00000243296 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715235.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243296	ENST00000715235.1		n.51+1851A>G		intron	N/A
	ENSG00000299024	ENST00000759926.1		n.214-3426T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.497 AC: 74914 AN: 150594 Hom.: 22841 Cov.: 30

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.497 AC: 74878 AN: 150680 Hom.: 22820 Cov.: 30 AF XY: 0.499 AC XY: 36694 AN XY: 73496

African (AFR) AF: 0.133 AC: 5489 AN: 41246

American (AMR) AF: 0.558 AC: 8408 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2798 AN: 3458

East Asian (EAS) AF: 0.454 AC: 2325 AN: 5120

South Asian (SAS) AF: 0.555 AC: 2652 AN: 4780

European-Finnish (FIN) AF: 0.669 AC: 6698 AN: 10018

Middle Eastern (MID) AF: 0.691 AC: 199 AN: 288

European-Non Finnish (NFE) AF: 0.660 AC: 44672 AN: 67704

Other (OTH) AF: 0.534 AC: 1117 AN: 2090

Alfa AF: 0.617 Hom.: 91069

Bravo AF: 0.475

Asia WGS AF: 0.464 AC: 1612 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.58
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs9861463; hg19: chr3-99052147;