rs2126200

Variant names:

• chr11-123002368-C-G
• rs2126200

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.479 in 151,956 control chromosomes in the GnomAD database, including 17,741 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 (17741 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.606 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: 0.479 AC: 72677 AN: 151838 Hom.: 17713 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.479 AC: 72755 AN: 151956 Hom.: 17741 Cov.: 31 AF XY: 0.485 AC XY: 36021 AN XY: 74260

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.480

Alfa AF: 0.459 Hom.: 1992

Bravo AF: 0.488

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2126200; hg19: chr11-122873076;