rs558240

Variant names:

• chr9-133281560-G-A
• rs558240

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 0.324 in 151,984 control chromosomes in the GnomAD database, including 8,592 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 0.32 (8592 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 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: 0.324 AC: 49270 AN: 151866 Hom.: 8594 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.324 AC: 49265 AN: 151984 Hom.: 8592 Cov.: 31 AF XY: 0.318 AC XY: 23587 AN XY: 74284

African (AFR) AF: 0.228 AC: 9461 AN: 41456

American (AMR) AF: 0.295 AC: 4501 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3470

East Asian (EAS) AF: 0.147 AC: 762 AN: 5174

South Asian (SAS) AF: 0.247 AC: 1192 AN: 4818

European-Finnish (FIN) AF: 0.335 AC: 3535 AN: 10562

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27172 AN: 67926

Other (OTH) AF: 0.351 AC: 740 AN: 2108

Alfa AF: 0.374 Hom.: 2443

Bravo AF: 0.318

Asia WGS AF: 0.201 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.79
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs558240; hg19: chr9-136157133;