rs3808850

Variant names:

• chr9-4983311-T-A
• rs3808850

Your query was ambiguous. Multiple possible variants found:

• chr9-4983311-T-A
• chr9-4983311-T-C

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 0.272 in 152,192 control chromosomes in the GnomAD database, including 6,469 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 0.27 (6469 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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: 0.272 AC: 41351 AN: 152074 Hom.: 6474 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.272 AC: 41360 AN: 152192 Hom.: 6469 Cov.: 33 AF XY: 0.274 AC XY: 20354 AN XY: 74380

African (AFR) AF: 0.110 AC: 4552 AN: 41564

American (AMR) AF: 0.281 AC: 4292 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2150 AN: 5178

South Asian (SAS) AF: 0.331 AC: 1599 AN: 4826

European-Finnish (FIN) AF: 0.354 AC: 3736 AN: 10556

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23330 AN: 67988

Other (OTH) AF: 0.279 AC: 590 AN: 2112

Alfa AF: 0.192 Hom.: 460

Bravo AF: 0.262

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs3808850; hg19: chr9-4983311;