rs487355

Variant names:

• chr18-77656645-G-A
• rs487355

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 0.106 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

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 = 0.479 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: 0.106 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

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.0904

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0847

Gnomad4 OTH AF: 0.0988

Alfa AF: 0.0888 Hom.: 1012

Bravo AF: 0.107

Asia WGS AF: 0.283 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs487355; hg19: chr18-75368601;