rs566618

Variant names:

• chr9-135043318-G-A
• rs566618

Your query was ambiguous. Multiple possible variants found:

• chr9-135043318-G-A
• chr9-135043318-G-C
• chr9-135043318-G-T

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 0.48 in 152,092 control chromosomes in the GnomAD database, including 18,072 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 0.48 (18072 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 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: 0.480 AC: 72955 AN: 151974 Hom.: 18044 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.480 AC: 73025 AN: 152092 Hom.: 18072 Cov.: 32 AF XY: 0.482 AC XY: 35837 AN XY: 74352

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.502

Alfa AF: 0.507 Hom.: 9354

Bravo AF: 0.480

Asia WGS AF: 0.617 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs566618; hg19: chr9-137935164;