chr2-146120874-A-G

Variant names:

• chr2-146120874-A-G
• rs222827

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 0.936 in 152,262 control chromosomes in the GnomAD database, including 66,929 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 (66929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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: 0.936 AC: 142368 AN: 152144 Hom.: 66897 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.936 AC: 142457 AN: 152262 Hom.: 66929 Cov.: 32 AF XY: 0.934 AC XY: 69541 AN XY: 74452

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.978

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.945

Alfa AF: 0.957 Hom.: 12452

Bravo AF: 0.926

Asia WGS AF: 0.919 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs222827; hg19: chr2-146878442;