18-12283548-A-G

Variant names:

• chr18-12283548-A-G
• rs7229921
• ENST00000772914.1:n.105+4474A>G

Variant summary

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

The ENST00000772914.1(ENSG00000267069):​n.105+4474A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,718 control chromosomes in the GnomAD database, including 4,721 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 0.25 (4721 hom., cov: 30)
• Consequence: ENSG00000267069 ENST00000772914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 7 publications found

Genes affected

ENSG00000267069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772914.1. 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
	ENSG00000267069	ENST00000772914.1		n.105+4474A>G		intron	N/A
	ENSG00000267069	ENST00000772915.1		n.334+3842A>G		intron	N/A
	ENSG00000267069	ENST00000772916.1		n.*239A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37503 AN: 151600 Hom.: 4695 Cov.: 30

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.248 AC: 37581 AN: 151718 Hom.: 4721 Cov.: 30 AF XY: 0.250 AC XY: 18520 AN XY: 74138

African (AFR) AF: 0.266 AC: 11023 AN: 41368

American (AMR) AF: 0.211 AC: 3220 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3468

East Asian (EAS) AF: 0.159 AC: 816 AN: 5146

South Asian (SAS) AF: 0.302 AC: 1441 AN: 4774

European-Finnish (FIN) AF: 0.280 AC: 2950 AN: 10528

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16708 AN: 67892

Other (OTH) AF: 0.246 AC: 517 AN: 2104

Alfa AF: 0.238 Hom.: 13301

Bravo AF: 0.240

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-0.10

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: rs7229921;

hg19: chr18-12283547;