rs2217560

chr18-72483704-G-Achr18-72483704-G-Cchr18-72483704-G-T

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 0.807 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.830

Alfa AF: 0.884 Hom.: 27287

Bravo AF: 0.792

Asia WGS AF: 0.796 AC: 2769 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.7
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2217560; hg19: chr18-70150939;