rs3808871

Variant names:

• chr9-34591427-G-A
• rs3808871

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 0.22 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.151 AC: 6286 AN: 41578

American (AMR) AF: 0.273 AC: 4183 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3468

East Asian (EAS) AF: 0.148 AC: 767 AN: 5188

South Asian (SAS) AF: 0.244 AC: 1179 AN: 4832

European-Finnish (FIN) AF: 0.227 AC: 2409 AN: 10604

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16990 AN: 67990

Other (OTH) AF: 0.211 AC: 447 AN: 2116

Alfa AF: 0.242 Hom.: 611

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
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs3808871; hg19: chr9-34591425;