rs3829254

Variant names:

• chr11-9570930-A-G
• rs3829254

Your query was ambiguous. Multiple possible variants found:

• chr11-9570930-A-G
• chr11-9570930-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 0.264 in 152,134 control chromosomes in the GnomAD database, including 5,576 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 0.26 (5576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.263 AC: 40056 AN: 152016 Hom.: 5555 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.264 AC: 40134 AN: 152134 Hom.: 5576 Cov.: 32 AF XY: 0.264 AC XY: 19666 AN XY: 74372

African (AFR) AF: 0.358 AC: 14845 AN: 41468

American (AMR) AF: 0.250 AC: 3815 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1021 AN: 5186

South Asian (SAS) AF: 0.223 AC: 1077 AN: 4826

European-Finnish (FIN) AF: 0.243 AC: 2572 AN: 10582

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15614 AN: 67996

Other (OTH) AF: 0.221 AC: 467 AN: 2114

Alfa AF: 0.233 Hom.: 1432

Bravo AF: 0.265

Asia WGS AF: 0.225 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs3829254; hg19: chr11-9592477;