rs7569590

Variant names:

• chr2-41329302-C-A
• rs7569590

Your query was ambiguous. Multiple possible variants found:

• chr2-41329302-C-A
• chr2-41329302-C-G

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 0.762 in 152,062 control chromosomes in the GnomAD database, including 44,998 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 0.76 (44998 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• 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 = 0.934 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: 0.762 AC: 115718 AN: 151944 Hom.: 44926 Cov.: 31

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.762 AC: 115854 AN: 152062 Hom.: 44998 Cov.: 31 AF XY: 0.766 AC XY: 56907 AN XY: 74332

African (AFR) AF: 0.893 AC: 37094 AN: 41530

American (AMR) AF: 0.771 AC: 11773 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2386 AN: 3462

East Asian (EAS) AF: 0.956 AC: 4948 AN: 5176

South Asian (SAS) AF: 0.768 AC: 3707 AN: 4824

European-Finnish (FIN) AF: 0.761 AC: 8038 AN: 10562

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45438 AN: 67924

Other (OTH) AF: 0.746 AC: 1574 AN: 2110

Alfa AF: 0.753 Hom.: 7498

Bravo AF: 0.770

Asia WGS AF: 0.874 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.68
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs7569590; hg19: chr2-41556442;