rs9846911

Variant names:

• chr3-187500548-A-G
• rs9846911
• ENST00000832464.1:n.196+13472A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-187500548-A-G
• chr3-187500548-A-T

Variant summary

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

The ENST00000832464.1(ENSG00000308202):​n.196+13472A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,972 control chromosomes in the GnomAD database, including 16,853 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 0.46 (16853 hom., cov: 31)
• Consequence: ENSG00000308202 ENST00000832464.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805
• Publications: 11 publications found

Genes affected

ENSG00000308202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832464.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308202	ENST00000832464.1		n.196+13472A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69847 AN: 151856 Hom.: 16832 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.0717

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.460 AC: 69917 AN: 151972 Hom.: 16853 Cov.: 31 AF XY: 0.451 AC XY: 33535 AN XY: 74282

African (AFR) AF: 0.551 AC: 22804 AN: 41416

American (AMR) AF: 0.337 AC: 5152 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1629 AN: 3466

East Asian (EAS) AF: 0.0717 AC: 371 AN: 5176

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4822

European-Finnish (FIN) AF: 0.409 AC: 4320 AN: 10552

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32210 AN: 67936

Other (OTH) AF: 0.446 AC: 941 AN: 2112

Alfa AF: 0.463 Hom.: 75260

Bravo AF: 0.454

Asia WGS AF: 0.245 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.6
DANN	Benign	0.60
PhyloP100		0.81

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9846911;

hg19: chr3-187218336;