chr12-69028249-C-G

Variant names:

• chr12-69028249-C-G
• rs10784749
• ENST00000842813.1:n.423-11211C>G

Variant summary

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

The ENST00000842813.1(ENSG00000309659):​n.423-11211C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,152 control chromosomes in the GnomAD database, including 36,972 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 0.69 (36972 hom., cov: 33)
• Consequence: ENSG00000309659 ENST00000842813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 2 publications found

Genes affected

ENSG00000309659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842813.1. 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
	ENSG00000309659	ENST00000842813.1		n.423-11211C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104583 AN: 152034 Hom.: 36976 Cov.: 33

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.688 AC: 104606 AN: 152152 Hom.: 36972 Cov.: 33 AF XY: 0.692 AC XY: 51499 AN XY: 74380

African (AFR) AF: 0.520 AC: 21583 AN: 41478

American (AMR) AF: 0.701 AC: 10716 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2569 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2815 AN: 5158

South Asian (SAS) AF: 0.783 AC: 3779 AN: 4826

European-Finnish (FIN) AF: 0.800 AC: 8485 AN: 10602

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52233 AN: 68006

Other (OTH) AF: 0.706 AC: 1493 AN: 2114

Alfa AF: 0.726 Hom.: 5085

Bravo AF: 0.666

Asia WGS AF: 0.634 AC: 2205 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.42
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10784749; hg19: chr12-69422029; COSMIC: COSV70149629;