rs3808871

chr9-34591427-G-A

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 0.22 in 152,280 control chromosomes in the GnomAD database, including 3,889 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 0.22 (3889 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 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: 0.219 AC: 33399 AN: 152162 Hom.: 3882 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.220 AC: 33437 AN: 152280 Hom.: 3889 Cov.: 33 AF XY: 0.220 AC XY: 16392 AN XY: 74458

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.211

Alfa AF: 0.245 Hom.: 603

Bravo AF: 0.220

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	8.7
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3808871; hg19: chr9-34591425;