chr3-172467586-A-G

Variant names:

• chr3-172467586-A-G
• rs9881097

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 0.55 in 152,024 control chromosomes in the GnomAD database, including 23,307 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 0.55 (23307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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: 0.550 AC: 83606 AN: 151906 Hom.: 23276 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.550 AC: 83688 AN: 152024 Hom.: 23307 Cov.: 31 AF XY: 0.548 AC XY: 40741 AN XY: 74292

African (AFR) AF: 0.631 AC: 26164 AN: 41438

American (AMR) AF: 0.535 AC: 8180 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1935 AN: 3472

East Asian (EAS) AF: 0.388 AC: 2009 AN: 5176

South Asian (SAS) AF: 0.593 AC: 2859 AN: 4824

European-Finnish (FIN) AF: 0.522 AC: 5509 AN: 10562

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35240 AN: 67962

Other (OTH) AF: 0.554 AC: 1166 AN: 2106

Alfa AF: 0.529 Hom.: 82811

Bravo AF: 0.553

Asia WGS AF: 0.537 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.80
DANN	Benign	0.38
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9881097; hg19: chr3-172185376;