rs9880056

Variant names:

• chr3-53900959-T-C
• rs9880056

Your query was ambiguous. Multiple possible variants found:

• chr3-53900959-T-C
• chr3-53900959-T-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 0.327 in 152,048 control chromosomes in the GnomAD database, including 8,332 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 0.33 (8332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.327 AC: 49696 AN: 151930 Hom.: 8332 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.327 AC: 49724 AN: 152048 Hom.: 8332 Cov.: 32 AF XY: 0.329 AC XY: 24419 AN XY: 74318

African (AFR) AF: 0.348 AC: 14425 AN: 41446

American (AMR) AF: 0.305 AC: 4657 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2518 AN: 5168

South Asian (SAS) AF: 0.319 AC: 1537 AN: 4818

European-Finnish (FIN) AF: 0.297 AC: 3142 AN: 10568

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21441 AN: 67980

Other (OTH) AF: 0.295 AC: 622 AN: 2112

Alfa AF: 0.223 Hom.: 681

Bravo AF: 0.328

Asia WGS AF: 0.377 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.41
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs9880056; hg19: chr3-53934986;