rs3809729

Positions:

• chr17-11596523-A-C

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 0.202 in 152,156 control chromosomes in the GnomAD database, including 3,845 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 0.20 (3845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30717 AN: 152038 Hom.: 3847 Cov.: 32

Gnomad AFR AF: 0.0645

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.202 AC: 30717 AN: 152156 Hom.: 3845 Cov.: 32 AF XY: 0.210 AC XY: 15592 AN XY: 74400

Gnomad4 AFR AF: 0.0643

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.211

Alfa AF: 0.243 Hom.: 6655

Bravo AF: 0.189

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809729; hg19: chr17-11499840;