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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369421	XR_001748531.2	n.79+2069C>A		intron_variant	Intron 1 of 3
LOC105369421	XR_007062825.1	n.211-7973C>A		intron_variant	Intron 2 of 4
LOC105369421	XR_007062826.1	n.189-7973C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309946	ENST00000846114.1	n.246+19467C>A		intron_variant	Intron 2 of 2
ENSG00000309946	ENST00000846115.1	n.245-7973C>A		intron_variant	Intron 2 of 4
ENSG00000309946	ENST00000846116.1	n.248-15267C>A		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs12804247; hg19: chr11-86079342;