rs2806922

chr13-45943924-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;