18-65923913-A-G

Variant names:

• chr18-65923913-A-G
• rs2160595

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 0.599 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.599 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

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.594

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2160595; hg19: chr18-63591149;