rs487355

Variant names:

• chr18-77656645-G-A
• rs487355

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 0.106 in 152,188 control chromosomes in the GnomAD database, including 1,289 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 0.11 (1289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 0 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 = 0.479 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16138 AN: 152070 Hom.: 1286 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.106 AC: 16161 AN: 152188 Hom.: 1289 Cov.: 32 AF XY: 0.110 AC XY: 8218 AN XY: 74398

African (AFR) AF: 0.0907 AC: 3768 AN: 41526

American (AMR) AF: 0.0904 AC: 1383 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3470

East Asian (EAS) AF: 0.495 AC: 2560 AN: 5172

South Asian (SAS) AF: 0.131 AC: 632 AN: 4824

European-Finnish (FIN) AF: 0.135 AC: 1428 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0847 AC: 5760 AN: 67986

Other (OTH) AF: 0.0988 AC: 209 AN: 2116

Alfa AF: 0.0908 Hom.: 1879

Bravo AF: 0.107

Asia WGS AF: 0.283 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.73
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs487355; hg19: chr18-75368601;