chr3-11969689-A-G

Variant names:

• chr3-11969689-A-G
• rs305489

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 0.436 in 152,138 control chromosomes in the GnomAD database, including 14,693 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 0.44 (14693 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 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: 0.436 AC: 66217 AN: 152020 Hom.: 14660 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.436 AC: 66301 AN: 152138 Hom.: 14693 Cov.: 33 AF XY: 0.430 AC XY: 32017 AN XY: 74384

African (AFR) AF: 0.462 AC: 19186 AN: 41504

American (AMR) AF: 0.406 AC: 6210 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1992 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1753 AN: 5174

South Asian (SAS) AF: 0.226 AC: 1091 AN: 4818

European-Finnish (FIN) AF: 0.412 AC: 4365 AN: 10582

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30281 AN: 67978

Other (OTH) AF: 0.455 AC: 961 AN: 2112

Alfa AF: 0.311 Hom.: 795

Bravo AF: 0.438

Asia WGS AF: 0.342 AC: 1190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.43
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs305489; hg19: chr3-12011163;