rs489659

Variant names:

• chr18-7557911-T-C
• rs489659

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 0.265 in 151,972 control chromosomes in the GnomAD database, including 6,733 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 0.27 (6733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

ACMG classification

Verdict is Benign. Variant got -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 = 0.701 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: 0.265 AC: 40235 AN: 151852 Hom.: 6715 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.265 AC: 40297 AN: 151972 Hom.: 6733 Cov.: 32 AF XY: 0.271 AC XY: 20132 AN XY: 74282

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.260

Alfa AF: 0.209 Hom.: 2020

Bravo AF: 0.283

Asia WGS AF: 0.570 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs489659; hg19: chr18-7557909;