rs222811

Variant names:

• chr2-146133505-A-G
• rs222811

Your query was ambiguous. Multiple possible variants found:

• chr2-146133505-A-G
• chr2-146133505-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 0.943 in 152,248 control chromosomes in the GnomAD database, including 67,953 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 0.94 (67953 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.976 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: 0.943 AC: 143533 AN: 152130 Hom.: 67924 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.943 AC: 143619 AN: 152248 Hom.: 67953 Cov.: 32 AF XY: 0.941 AC XY: 70056 AN XY: 74434

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.967

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.978

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.949

Alfa AF: 0.962 Hom.: 15793

Bravo AF: 0.936

Asia WGS AF: 0.919 AC: 3197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.59
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs222811; hg19: chr2-146891073;