rs3809717

chr17-39730733-C-Achr17-39730733-C-Gchr17-39730733-C-T

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 0.267 in 526,334 control chromosomes in the GnomAD database, including 20,315 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 0.23 (4710 hom., cov: 32)
  • Exomes 𝑓: 0.28 (15605 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 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: 0.226 AC: 34332 AN: 152034 Hom.: 4710 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.246

GnomAD4 exome AF: 0.284 AC: 106278 AN: 374182 Hom.: 15605 Cov.: 3 AF XY: 0.281 AC XY: 55197 AN XY: 196424

Gnomad4 AFR exome AF: 0.0733

Gnomad4 AMR exome AF: 0.232

Gnomad4 ASJ exome AF: 0.309

Gnomad4 EAS exome AF: 0.261

Gnomad4 SAS exome AF: 0.233

Gnomad4 FIN exome AF: 0.331

Gnomad4 NFE exome AF: 0.297

Gnomad4 OTH exome AF: 0.275

GnomAD4 genome AF: 0.226 AC: 34340 AN: 152152 Hom.: 4710 Cov.: 32 AF XY: 0.228 AC XY: 16958 AN XY: 74364

Gnomad4 AFR AF: 0.0718

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.245

Alfa AF: 0.254 Hom.: 952

Bravo AF: 0.210

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	3.3
Dann	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.53		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.53		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809717; hg19: chr17-37886986;