chr18-2217798-A-G

Position:

• chr18-2217798-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.11 in 152,036 control chromosomes in the GnomAD database, including 1,363 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 0.11 (1363 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2217798A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000263745	ENST00000579097.1	n.88+21995T>C		intron_variant		2
ENSG00000263745	ENST00000584867.1	n.196+21995T>C		intron_variant		2
ENSG00000263745	ENST00000639316.2	n.441+21995T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16720 AN: 151918 Hom.: 1351 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.110 AC: 16765 AN: 152036 Hom.: 1363 Cov.: 32 AF XY: 0.114 AC XY: 8478 AN XY: 74340

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0992

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.0982

Gnomad4 FIN AF: 0.0857

Gnomad4 NFE AF: 0.0442

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0554 Hom.: 764

Bravo AF: 0.122

Asia WGS AF: 0.192 AC: 664 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.83
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8086568; hg19: chr18-2217798;