rs9877502

Variant names:

• chr3-190951729-G-A
• rs9877502

Your query was ambiguous. Multiple possible variants found:

• chr3-190951729-G-A
• chr3-190951729-G-C

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 0.396 in 151,858 control chromosomes in the GnomAD database, including 12,448 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 0.40 (12448 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.396 AC: 60087 AN: 151742 Hom.: 12437 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.311

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.396 AC: 60136 AN: 151858 Hom.: 12448 Cov.: 32 AF XY: 0.393 AC XY: 29133 AN XY: 74214

African (AFR) AF: 0.496 AC: 20534 AN: 41382

American (AMR) AF: 0.301 AC: 4596 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1760 AN: 5168

South Asian (SAS) AF: 0.220 AC: 1060 AN: 4826

European-Finnish (FIN) AF: 0.428 AC: 4500 AN: 10510

Middle Eastern (MID) AF: 0.328 AC: 95 AN: 290

European-Non Finnish (NFE) AF: 0.369 AC: 25046 AN: 67930

Other (OTH) AF: 0.368 AC: 778 AN: 2114

Alfa AF: 0.382 Hom.: 16383

Bravo AF: 0.394

Asia WGS AF: 0.301 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs9877502; hg19: chr3-190669518;