18-2217798-A-G

Variant names:

• chr18-2217798-A-G
• rs8086568
• ENST00000579097.1:n.88+21995T>C

Variant summary

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

The ENST00000579097.1(ENSG00000263745):​n.88+21995T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000263745 ENST00000579097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 1 publications found

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579097.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000263745	ENST00000579097.1	TSL:2	n.88+21995T>C		intron	N/A
	ENSG00000263745	ENST00000584867.1	TSL:2	n.196+21995T>C		intron	N/A
	ENSG00000263745	ENST00000639316.2	TSL:5	n.441+21995T>C		intron	N/A

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

African (AFR) AF: 0.190 AC: 7881 AN: 41490

American (AMR) AF: 0.150 AC: 2286 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0992 AC: 344 AN: 3466

East Asian (EAS) AF: 0.310 AC: 1599 AN: 5162

South Asian (SAS) AF: 0.0982 AC: 474 AN: 4828

European-Finnish (FIN) AF: 0.0857 AC: 909 AN: 10608

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3003 AN: 67936

Other (OTH) AF: 0.100 AC: 211 AN: 2108

Alfa AF: 0.0645 Hom.: 2192

Bravo AF: 0.122

Asia WGS AF: 0.192 AC: 664 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.83
DANN	Benign	0.56
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs8086568; hg19: chr18-2217798;