rs9304560

Variant names:

• chr18-30516558-A-G
• rs9304560

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 0.352 in 152,084 control chromosomes in the GnomAD database, including 9,706 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 0.35 (9706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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: 0.352 AC: 53469 AN: 151970 Hom.: 9693 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.352 AC: 53515 AN: 152084 Hom.: 9706 Cov.: 32 AF XY: 0.347 AC XY: 25782 AN XY: 74338

African (AFR) AF: 0.369 AC: 15316 AN: 41480

American (AMR) AF: 0.243 AC: 3711 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3468

East Asian (EAS) AF: 0.165 AC: 853 AN: 5174

South Asian (SAS) AF: 0.313 AC: 1511 AN: 4822

European-Finnish (FIN) AF: 0.393 AC: 4164 AN: 10586

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25800 AN: 67966

Other (OTH) AF: 0.321 AC: 678 AN: 2112

Alfa AF: 0.378 Hom.: 1422

Bravo AF: 0.339

Asia WGS AF: 0.235 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9304560; hg19: chr18-28096524;