rs2199232

Variant names:

• chr11-21714279-C-T
• rs2199232

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 0.486 in 151,892 control chromosomes in the GnomAD database, including 18,191 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 (18191 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 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: 0.486 AC: 73708 AN: 151776 Hom.: 18162 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.486 AC: 73787 AN: 151892 Hom.: 18191 Cov.: 32 AF XY: 0.488 AC XY: 36240 AN XY: 74210

African (AFR) AF: 0.533 AC: 22074 AN: 41414

American (AMR) AF: 0.577 AC: 8808 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3472

East Asian (EAS) AF: 0.570 AC: 2940 AN: 5158

South Asian (SAS) AF: 0.506 AC: 2432 AN: 4808

European-Finnish (FIN) AF: 0.434 AC: 4557 AN: 10504

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29993 AN: 67954

Other (OTH) AF: 0.469 AC: 989 AN: 2110

Alfa AF: 0.474 Hom.: 2140

Bravo AF: 0.498

Asia WGS AF: 0.492 AC: 1709 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.19
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs2199232; hg19: chr11-21735825;