rs3809729

Variant names:

• chr17-11596523-A-C
• rs3809729

Your query was ambiguous. Multiple possible variants found:

• chr17-11596523-A-C
• chr17-11596523-A-G
• chr17-11596523-A-T

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 0.202 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0643 AC: 2671 AN: 41546

American (AMR) AF: 0.261 AC: 3994 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3468

East Asian (EAS) AF: 0.148 AC: 764 AN: 5174

South Asian (SAS) AF: 0.363 AC: 1749 AN: 4820

European-Finnish (FIN) AF: 0.308 AC: 3260 AN: 10576

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16599 AN: 67972

Other (OTH) AF: 0.211 AC: 446 AN: 2116

Alfa AF: 0.228 Hom.: 9455

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs3809729; hg19: chr17-11499840;