2-146120874-A-G

Variant names:

• chr2-146120874-A-G
• rs222827

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.856 AC: 35569 AN: 41542

American (AMR) AF: 0.898 AC: 13720 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3455 AN: 3472

East Asian (EAS) AF: 0.966 AC: 4999 AN: 5174

South Asian (SAS) AF: 0.909 AC: 4387 AN: 4824

European-Finnish (FIN) AF: 0.978 AC: 10390 AN: 10624

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66818 AN: 68030

Other (OTH) AF: 0.945 AC: 1998 AN: 2114

Alfa AF: 0.958 Hom.: 22530

Bravo AF: 0.926

Asia WGS AF: 0.919 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.78
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs222827; hg19: chr2-146878442;