18-60191833-A-G

Variant names:

• chr18-60191833-A-G
• rs619825

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 0.467 in 152,006 control chromosomes in the GnomAD database, including 18,718 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 0.47 (18718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 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: 0.466 AC: 70834 AN: 151888 Hom.: 18673 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.467 AC: 70931 AN: 152006 Hom.: 18718 Cov.: 32 AF XY: 0.459 AC XY: 34128 AN XY: 74304

African (AFR) AF: 0.723 AC: 29973 AN: 41460

American (AMR) AF: 0.325 AC: 4969 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3466

East Asian (EAS) AF: 0.216 AC: 1116 AN: 5176

South Asian (SAS) AF: 0.486 AC: 2341 AN: 4814

European-Finnish (FIN) AF: 0.345 AC: 3640 AN: 10564

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26443 AN: 67940

Other (OTH) AF: 0.431 AC: 909 AN: 2110

Alfa AF: 0.408 Hom.: 17279

Bravo AF: 0.474

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.6
DANN	Benign	0.88
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs619825; hg19: chr18-57859066;