rs1568573

Variant names:

• chr3-160740227-C-A
• rs1568573

Your query was ambiguous. Multiple possible variants found:

• chr3-160740227-C-A
• chr3-160740227-C-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 0.314 in 152,036 control chromosomes in the GnomAD database, including 7,667 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 0.31 (7667 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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: 0.315 AC: 47788 AN: 151918 Hom.: 7665 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.314 AC: 47811 AN: 152036 Hom.: 7667 Cov.: 33 AF XY: 0.313 AC XY: 23231 AN XY: 74304

African (AFR) AF: 0.345 AC: 14292 AN: 41468

American (AMR) AF: 0.310 AC: 4729 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 682 AN: 3468

East Asian (EAS) AF: 0.506 AC: 2622 AN: 5182

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4822

European-Finnish (FIN) AF: 0.289 AC: 3049 AN: 10544

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

European-Non Finnish (NFE) AF: 0.299 AC: 20352 AN: 67962

Other (OTH) AF: 0.255 AC: 537 AN: 2110

Alfa AF: 0.280 Hom.: 3394

Bravo AF: 0.319

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.74
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs1568573; hg19: chr3-160458015;