rs259822

Variant names:

• chr2-179910977-A-G
• rs259822

Your query was ambiguous. Multiple possible variants found:

• chr2-179910977-A-G
• chr2-179910977-A-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 0.43 in 152,068 control chromosomes in the GnomAD database, including 15,756 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 0.43 (15756 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 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: 0.430 AC: 65334 AN: 151950 Hom.: 15722 Cov.: 33

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.430 AC: 65415 AN: 152068 Hom.: 15756 Cov.: 33 AF XY: 0.429 AC XY: 31865 AN XY: 74318

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.387

Alfa AF: 0.340 Hom.: 14203

Bravo AF: 0.445

Asia WGS AF: 0.259 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs259822; hg19: chr2-180775704;