rs9846284

Variant names:

• chr3-45315474-G-A
• rs9846284
• ENST00000756647.1:n.34+3187G>A

Variant summary

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

The ENST00000756647.1(ENSG00000298579):​n.34+3187G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 152,238 control chromosomes in the GnomAD database, including 696 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 0.057 (696 hom., cov: 32)
• Consequence: ENSG00000298579 ENST00000756647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 1 publications found

Genes affected

ENSG00000298579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756647.1. 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
	ENSG00000298579	ENST00000756647.1		n.34+3187G>A		intron	N/A
	ENSG00000298579	ENST00000756648.1		n.46+3187G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0562 AC: 8550 AN: 152120 Hom.: 689 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.00318

Gnomad EAS AF: 0.0242

Gnomad SAS AF: 0.0783

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00294

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0565 AC: 8602 AN: 152238 Hom.: 696 Cov.: 32 AF XY: 0.0562 AC XY: 4183 AN XY: 74450

African (AFR) AF: 0.179 AC: 7434 AN: 41502

American (AMR) AF: 0.0234 AC: 358 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00318 AC: 11 AN: 3462

East Asian (EAS) AF: 0.0241 AC: 125 AN: 5188

South Asian (SAS) AF: 0.0784 AC: 378 AN: 4822

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10620

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00294 AC: 200 AN: 68020

Other (OTH) AF: 0.0425 AC: 90 AN: 2116

Alfa AF: 0.0392 Hom.: 66

Bravo AF: 0.0627

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs9846284; hg19: chr3-45356966;