rs11680709

Variant names:

• chr2-219185985-G-A
• rs11680709

Your query was ambiguous. Multiple possible variants found:

• chr2-219185985-G-A
• chr2-219185985-G-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 0.482 in 151,992 control chromosomes in the GnomAD database, including 19,122 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 0.48 (19122 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.59 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: 0.482 AC: 73244 AN: 151874 Hom.: 19126 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.482 AC: 73255 AN: 151992 Hom.: 19122 Cov.: 33 AF XY: 0.483 AC XY: 35903 AN XY: 74296

African (AFR) AF: 0.286 AC: 11844 AN: 41438

American (AMR) AF: 0.436 AC: 6655 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2104 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1391 AN: 5158

South Asian (SAS) AF: 0.565 AC: 2729 AN: 4826

European-Finnish (FIN) AF: 0.615 AC: 6499 AN: 10562

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.595 AC: 40396 AN: 67946

Other (OTH) AF: 0.478 AC: 1010 AN: 2112

Alfa AF: 0.411 Hom.: 1237

Bravo AF: 0.454

Asia WGS AF: 0.347 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.25
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11680709; hg19: chr2-220050707;