rs12804247

Variant names:

• chr11-86368300-G-T
• rs12804247
• ENST00000846114.1:n.246+19467C>A

Variant summary

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

The ENST00000846114.1(ENSG00000309946):​n.246+19467C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,020 control chromosomes in the GnomAD database, including 2,780 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 0.17 (2780 hom., cov: 33)
• Consequence: ENSG00000309946 ENST00000846114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 2 publications found

Genes affected

ENSG00000309946 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846114.1. 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
	ENSG00000309946	ENST00000846114.1		n.246+19467C>A		intron	N/A
	ENSG00000309946	ENST00000846115.1		n.245-7973C>A		intron	N/A
	ENSG00000309946	ENST00000846116.1		n.248-15267C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25593 AN: 151902 Hom.: 2778 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.0979

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.169 AC: 25618 AN: 152020 Hom.: 2780 Cov.: 33 AF XY: 0.170 AC XY: 12669 AN XY: 74306

African (AFR) AF: 0.245 AC: 10176 AN: 41470

American (AMR) AF: 0.212 AC: 3241 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3470

East Asian (EAS) AF: 0.471 AC: 2446 AN: 5190

South Asian (SAS) AF: 0.240 AC: 1155 AN: 4808

European-Finnish (FIN) AF: 0.0556 AC: 588 AN: 10578

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.0979 AC: 6649 AN: 67910

Other (OTH) AF: 0.170 AC: 360 AN: 2114

Alfa AF: 0.128 Hom.: 832

Bravo AF: 0.187

Asia WGS AF: 0.289 AC: 1000 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.15
PhyloP100		-0.34

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: rs12804247;

hg19: chr11-86079342;