rs2033518

Variant names:

• chr3-426100-C-G
• rs2033518

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 0.872 in 152,240 control chromosomes in the GnomAD database, including 60,393 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 0.87 (60393 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 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: 0.872 AC: 132619 AN: 152122 Hom.: 60371 Cov.: 34

Gnomad AFR AF: 0.575

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.972

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.872 AC: 132685 AN: 152240 Hom.: 60393 Cov.: 34 AF XY: 0.875 AC XY: 65098 AN XY: 74436

African (AFR) AF: 0.575 AC: 23871 AN: 41494

American (AMR) AF: 0.931 AC: 14219 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3446 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5182 AN: 5184

South Asian (SAS) AF: 0.973 AC: 4701 AN: 4832

European-Finnish (FIN) AF: 1.00 AC: 10621 AN: 10626

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67590 AN: 68036

Other (OTH) AF: 0.890 AC: 1879 AN: 2112

Alfa AF: 0.921 Hom.: 8252

Bravo AF: 0.853

Asia WGS AF: 0.956 AC: 3323 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.63
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs2033518; hg19: chr3-467783;