rs4878538

Variant names:

• chr9-33425387-G-A
• rs4878538

Your query was ambiguous. Multiple possible variants found:

• chr9-33425387-G-A
• chr9-33425387-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 0.393 in 152,058 control chromosomes in the GnomAD database, including 12,053 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 0.39 (12053 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 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: 0.393 AC: 59744 AN: 151940 Hom.: 12038 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.393 AC: 59799 AN: 152058 Hom.: 12053 Cov.: 33 AF XY: 0.390 AC XY: 28987 AN XY: 74330

African (AFR) AF: 0.313 AC: 12960 AN: 41466

American (AMR) AF: 0.379 AC: 5784 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1782 AN: 5168

South Asian (SAS) AF: 0.315 AC: 1521 AN: 4832

European-Finnish (FIN) AF: 0.424 AC: 4477 AN: 10568

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30527 AN: 67958

Other (OTH) AF: 0.396 AC: 838 AN: 2116

Alfa AF: 0.418 Hom.: 26258

Bravo AF: 0.385

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.93
DANN	Benign	0.46
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4878538; hg19: chr9-33425385;