rs2216924

Positions:

• chr2-66852811-C-A

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 0.279 in 152,018 control chromosomes in the GnomAD database, including 5,989 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 0.28 (5989 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 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: 0.279 AC: 42415 AN: 151898 Hom.: 5985 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.279 AC: 42457 AN: 152018 Hom.: 5989 Cov.: 33 AF XY: 0.279 AC XY: 20708 AN XY: 74278

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.274

Alfa AF: 0.284 Hom.: 1104

Bravo AF: 0.273

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2216924; hg19: chr2-67079943;