rs9989529

Variant names:

• chr18-63114144-T-C
• rs9989529

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 0.379 in 152,044 control chromosomes in the GnomAD database, including 12,027 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 0.38 (12027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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: 0.379 AC: 57651 AN: 151928 Hom.: 12024 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.379 AC: 57672 AN: 152044 Hom.: 12027 Cov.: 32 AF XY: 0.378 AC XY: 28087 AN XY: 74336

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.379

Alfa AF: 0.448 Hom.: 17325

Bravo AF: 0.352

Asia WGS AF: 0.238 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9989529; hg19: chr18-60781377;