rs2806922

Variant names:

• chr13-45943924-C-T
• rs2806922

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 0.268 in 152,122 control chromosomes in the GnomAD database, including 5,723 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 0.27 (5723 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 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: 0.268 AC: 40804 AN: 152004 Hom.: 5714 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.268 AC: 40835 AN: 152122 Hom.: 5723 Cov.: 33 AF XY: 0.263 AC XY: 19572 AN XY: 74370

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.317

Alfa AF: 0.275 Hom.: 1004

Bravo AF: 0.271

Asia WGS AF: 0.240 AC: 833 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2806922; hg19: chr13-46518059; COSMIC: COSV69348967;