rs11899121

Variant names:

• chr2-20168212-G-C
• rs11899121

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 0.495 in 152,004 control chromosomes in the GnomAD database, including 18,740 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 0.49 (18740 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.54 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: 0.495 AC: 75145 AN: 151886 Hom.: 18731 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.495 AC: 75182 AN: 152004 Hom.: 18740 Cov.: 32 AF XY: 0.500 AC XY: 37121 AN XY: 74282

African (AFR) AF: 0.508 AC: 21078 AN: 41460

American (AMR) AF: 0.467 AC: 7145 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2040 AN: 5152

South Asian (SAS) AF: 0.558 AC: 2682 AN: 4808

European-Finnish (FIN) AF: 0.593 AC: 6272 AN: 10574

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33021 AN: 67940

Other (OTH) AF: 0.458 AC: 968 AN: 2112

Alfa AF: 0.506 Hom.: 2454

Bravo AF: 0.484

Asia WGS AF: 0.458 AC: 1597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.43
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs11899121; hg19: chr2-20367973;