18-60065457-A-G

Variant names:

• chr18-60065457-A-G
• rs4940927

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 0.689 in 152,048 control chromosomes in the GnomAD database, including 37,082 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 0.69 (37082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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: 0.690 AC: 104766 AN: 151928 Hom.: 37068 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.689 AC: 104829 AN: 152048 Hom.: 37082 Cov.: 32 AF XY: 0.695 AC XY: 51653 AN XY: 74338

African (AFR) AF: 0.526 AC: 21807 AN: 41430

American (AMR) AF: 0.791 AC: 12073 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2606 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4305 AN: 5172

South Asian (SAS) AF: 0.651 AC: 3131 AN: 4812

European-Finnish (FIN) AF: 0.822 AC: 8707 AN: 10594

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49904 AN: 67978

Other (OTH) AF: 0.703 AC: 1484 AN: 2112

Alfa AF: 0.695 Hom.: 25938

Bravo AF: 0.681

Asia WGS AF: 0.774 AC: 2692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.84
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4940927; hg19: chr18-57732689;