rs2033518

chr3-426100-C-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.993

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.890

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2033518; hg19: chr3-467783;