3-88561313-G-A

Variant names:

• chr3-88561313-G-A
• rs10525576

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.26 (4321 hom., cov: 15)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.263 AC: 30318 AN: 115202 Hom.: 4322 Cov.: 15

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.302

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.263 AC: 30310 AN: 115190 Hom.: 4321 Cov.: 15 AF XY: 0.266 AC XY: 14124 AN XY: 53104

African (AFR) AF: 0.177 AC: 5491 AN: 31028

American (AMR) AF: 0.278 AC: 2629 AN: 9458

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1172 AN: 3112

East Asian (EAS) AF: 0.191 AC: 773 AN: 4042

South Asian (SAS) AF: 0.189 AC: 632 AN: 3340

European-Finnish (FIN) AF: 0.420 AC: 1312 AN: 3122

Middle Eastern (MID) AF: 0.299 AC: 55 AN: 184

European-Non Finnish (NFE) AF: 0.299 AC: 17531 AN: 58550

Other (OTH) AF: 0.256 AC: 397 AN: 1548

Alfa AF: 0.312 Hom.: 654

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.64
DANN	Benign	0.32
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs10525576; hg19: chr3-88610463;