5-30785933-A-G

Variant names:

• chr5-30785933-A-G
• rs2133764

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 0.846 in 152,090 control chromosomes in the GnomAD database, including 54,752 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 0.85 (54752 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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: 0.846 AC: 128611 AN: 151972 Hom.: 54690 Cov.: 31

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.846 AC: 128732 AN: 152090 Hom.: 54752 Cov.: 31 AF XY: 0.847 AC XY: 62985 AN XY: 74324

African (AFR) AF: 0.903 AC: 37506 AN: 41514

American (AMR) AF: 0.850 AC: 12960 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2997 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5026 AN: 5162

South Asian (SAS) AF: 0.907 AC: 4376 AN: 4826

European-Finnish (FIN) AF: 0.750 AC: 7939 AN: 10586

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55194 AN: 67964

Other (OTH) AF: 0.850 AC: 1794 AN: 2110

Alfa AF: 0.817 Hom.: 22434

Bravo AF: 0.858

Asia WGS AF: 0.939 AC: 3262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.25
DANN	Benign	0.22
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2133764; hg19: chr5-30786040;