rs12709669

Variant names:

• chr18-22227108-T-G
• rs12709669
• ENST00000578741.1:n.224-779T>G

Variant summary

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

The ENST00000578741.1(ENSG00000264825):​n.224-779T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,104 control chromosomes in the GnomAD database, including 24,203 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 0.56 (24203 hom., cov: 33)
• Consequence: ENSG00000264825 ENST00000578741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 5 publications found

Genes affected

ENSG00000264825 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000578741.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000264825	ENST00000578741.1	TSL:3	n.224-779T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85147 AN: 151988 Hom.: 24170 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.560 AC: 85241 AN: 152104 Hom.: 24203 Cov.: 33 AF XY: 0.558 AC XY: 41513 AN XY: 74360

African (AFR) AF: 0.627 AC: 26010 AN: 41478

American (AMR) AF: 0.578 AC: 8849 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1799 AN: 3472

East Asian (EAS) AF: 0.437 AC: 2256 AN: 5160

South Asian (SAS) AF: 0.539 AC: 2600 AN: 4822

European-Finnish (FIN) AF: 0.503 AC: 5318 AN: 10582

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36628 AN: 67976

Other (OTH) AF: 0.546 AC: 1153 AN: 2110

Alfa AF: 0.571 Hom.: 4818

Bravo AF: 0.571

Asia WGS AF: 0.481 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12709669; hg19: chr18-19807071;