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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.375 AC: 15553 AN: 41462

American (AMR) AF: 0.526 AC: 8043 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3472

East Asian (EAS) AF: 0.735 AC: 3814 AN: 5186

South Asian (SAS) AF: 0.629 AC: 3031 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4784 AN: 10580

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34327 AN: 67974

Other (OTH) AF: 0.502 AC: 1062 AN: 2114

Alfa AF: 0.506 Hom.: 10395

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs566618; hg19: chr9-137935164;