rs9849690

Variant names:

• chr3-184610232-G-A
• rs9849690
• ENST00000806394.1:n.316-6648G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-184610232-G-A
• chr3-184610232-G-C

Variant summary

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

The ENST00000806394.1(ENSG00000304807):​n.316-6648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,782 control chromosomes in the GnomAD database, including 16,827 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 0.47 (16827 hom., cov: 30)
• Consequence: ENSG00000304807 ENST00000806394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 5 publications found

Genes affected

ENSG00000304807 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806394.1. 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
	ENSG00000304807	ENST00000806394.1		n.316-6648G>A		intron	N/A
	ENSG00000304807	ENST00000806395.1		n.352-5575G>A		intron	N/A
	ENSG00000304807	ENST00000806396.1		n.371-5575G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70553 AN: 151664 Hom.: 16810 Cov.: 30

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.465 AC: 70607 AN: 151782 Hom.: 16827 Cov.: 30 AF XY: 0.468 AC XY: 34708 AN XY: 74190

African (AFR) AF: 0.425 AC: 17586 AN: 41360

American (AMR) AF: 0.428 AC: 6541 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1730 AN: 3470

East Asian (EAS) AF: 0.526 AC: 2705 AN: 5142

South Asian (SAS) AF: 0.373 AC: 1796 AN: 4818

European-Finnish (FIN) AF: 0.552 AC: 5812 AN: 10538

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32792 AN: 67876

Other (OTH) AF: 0.479 AC: 1010 AN: 2108

Alfa AF: 0.473 Hom.: 30237

Bravo AF: 0.457

Asia WGS AF: 0.460 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.44
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9849690; hg19: chr3-184328020;