18-65923913-A-G

Variant names:

• chr18-65923913-A-G
• rs2160595

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 0.599 in 151,982 control chromosomes in the GnomAD database, including 27,588 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 0.60 (27588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

 

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

Frequencies

GnomAD3 genomes AF: 0.599 AC: 91005 AN: 151864 Hom.: 27574 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.599 AC: 91069 AN: 151982 Hom.: 27588 Cov.: 32 AF XY: 0.603 AC XY: 44796 AN XY: 74272

African (AFR) AF: 0.512 AC: 21222 AN: 41452

American (AMR) AF: 0.620 AC: 9465 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2320 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3609 AN: 5166

South Asian (SAS) AF: 0.593 AC: 2860 AN: 4826

European-Finnish (FIN) AF: 0.641 AC: 6763 AN: 10550

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.629 AC: 42765 AN: 67956

Other (OTH) AF: 0.594 AC: 1248 AN: 2102

Alfa AF: 0.477 Hom.: 1302

Bravo AF: 0.593

Asia WGS AF: 0.603 AC: 2078 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.80
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2160595; hg19: chr18-63591149;