rs2217560

Variant names:

• chr18-72483704-G-A
• rs2217560

Your query was ambiguous. Multiple possible variants found:

• chr18-72483704-G-A
• chr18-72483704-G-C
• chr18-72483704-G-T

Variant summary

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

The variant allele was found at a frequency of 0.807 in 152,200 control chromosomes in the GnomAD database, including 51,492 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 0.81 (51492 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122830 AN: 152082 Hom.: 51463 Cov.: 34

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.807 AC: 122900 AN: 152200 Hom.: 51492 Cov.: 34 AF XY: 0.811 AC XY: 60313 AN XY: 74408

African (AFR) AF: 0.558 AC: 23146 AN: 41484

American (AMR) AF: 0.886 AC: 13534 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3168 AN: 3472

East Asian (EAS) AF: 0.772 AC: 3991 AN: 5172

South Asian (SAS) AF: 0.827 AC: 3993 AN: 4828

European-Finnish (FIN) AF: 0.942 AC: 10003 AN: 10614

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.915 AC: 62231 AN: 68030

Other (OTH) AF: 0.830 AC: 1757 AN: 2116

Alfa AF: 0.867 Hom.: 115929

Bravo AF: 0.792

Asia WGS AF: 0.796 AC: 2769 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.63
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs2217560; hg19: chr18-70150939;