rs9819506

Variant names:

• chr3-172452314-C-T
• rs9819506

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 0.356 in 151,838 control chromosomes in the GnomAD database, including 10,124 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 0.36 (10124 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.728
• Publications: 11 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 = 0.453 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: 0.356 AC: 54024 AN: 151720 Hom.: 10113 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.356 AC: 54075 AN: 151838 Hom.: 10124 Cov.: 31 AF XY: 0.361 AC XY: 26779 AN XY: 74224

African (AFR) AF: 0.459 AC: 18971 AN: 41368

American (AMR) AF: 0.322 AC: 4919 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1218 AN: 3460

East Asian (EAS) AF: 0.367 AC: 1896 AN: 5168

South Asian (SAS) AF: 0.457 AC: 2201 AN: 4818

European-Finnish (FIN) AF: 0.381 AC: 4017 AN: 10542

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.289 AC: 19610 AN: 67922

Other (OTH) AF: 0.348 AC: 732 AN: 2104

Alfa AF: 0.313 Hom.: 24026

Bravo AF: 0.354

Asia WGS AF: 0.437 AC: 1514 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.32
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs9819506; hg19: chr3-172170104;