rs3806566

Variant names:

• chr2-171520546-A-G
• rs3806566

Your query was ambiguous. Multiple possible variants found:

• chr2-171520546-A-G
• chr2-171520546-A-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 0.219 in 152,108 control chromosomes in the GnomAD database, including 4,280 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 0.22 (4280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 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: 0.219 AC: 33309 AN: 151990 Hom.: 4268 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.219 AC: 33350 AN: 152108 Hom.: 4280 Cov.: 31 AF XY: 0.221 AC XY: 16420 AN XY: 74370

African (AFR) AF: 0.356 AC: 14776 AN: 41466

American (AMR) AF: 0.152 AC: 2321 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 446 AN: 3472

East Asian (EAS) AF: 0.142 AC: 734 AN: 5174

South Asian (SAS) AF: 0.161 AC: 775 AN: 4818

European-Finnish (FIN) AF: 0.249 AC: 2632 AN: 10588

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11102 AN: 67990

Other (OTH) AF: 0.188 AC: 396 AN: 2112

Alfa AF: 0.183 Hom.: 999

Bravo AF: 0.218

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.8
DANN	Benign	0.54
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs3806566; hg19: chr2-172377056;