3-172467586-A-G

Variant names:

• chr3-172467586-A-G
• rs9881097

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.554

Alfa AF: 0.526 Hom.: 35644

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9881097; hg19: chr3-172185376;