18-72897259-A-C

Variant names:

• chr18-72897259-A-C
• rs2187113

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 0.86 in 152,130 control chromosomes in the GnomAD database, including 57,493 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 0.86 (57493 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130704 AN: 152012 Hom.: 57469 Cov.: 33

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.860 AC: 130780 AN: 152130 Hom.: 57493 Cov.: 33 AF XY: 0.860 AC XY: 63951 AN XY: 74378

African (AFR) AF: 0.661 AC: 27407 AN: 41446

American (AMR) AF: 0.894 AC: 13666 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3253 AN: 3472

East Asian (EAS) AF: 0.693 AC: 3576 AN: 5158

South Asian (SAS) AF: 0.871 AC: 4205 AN: 4826

European-Finnish (FIN) AF: 0.966 AC: 10234 AN: 10598

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.962 AC: 65448 AN: 68026

Other (OTH) AF: 0.879 AC: 1860 AN: 2116

Alfa AF: 0.907 Hom.: 7446

Bravo AF: 0.847

Asia WGS AF: 0.808 AC: 2809 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2187113; hg19: chr18-70564494;