rs1505618

Variant names:

• chr9-78553302-A-G
• rs1505618

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 0.261 in 152,188 control chromosomes in the GnomAD database, including 5,456 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 0.26 (5456 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39668 AN: 152070 Hom.: 5457 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.261 AC: 39682 AN: 152188 Hom.: 5456 Cov.: 33 AF XY: 0.257 AC XY: 19087 AN XY: 74398

African (AFR) AF: 0.190 AC: 7899 AN: 41536

American (AMR) AF: 0.271 AC: 4147 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3470

East Asian (EAS) AF: 0.117 AC: 608 AN: 5176

South Asian (SAS) AF: 0.258 AC: 1243 AN: 4816

European-Finnish (FIN) AF: 0.278 AC: 2945 AN: 10594

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21392 AN: 67986

Other (OTH) AF: 0.250 AC: 529 AN: 2112

Alfa AF: 0.299 Hom.: 12587

Bravo AF: 0.256

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.53
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1505618; hg19: chr9-81168218;