2-219857977-G-A

Variant names:

• chr2-219857977-G-A
• rs10498071

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 0.0922 in 152,238 control chromosomes in the GnomAD database, including 695 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 0.092 (695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14023 AN: 152120 Hom.: 692 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0885

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0922 AC: 14035 AN: 152238 Hom.: 695 Cov.: 32 AF XY: 0.0894 AC XY: 6657 AN XY: 74438

African (AFR) AF: 0.113 AC: 4708 AN: 41542

American (AMR) AF: 0.0736 AC: 1125 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3470

East Asian (EAS) AF: 0.133 AC: 692 AN: 5184

South Asian (SAS) AF: 0.0602 AC: 290 AN: 4814

European-Finnish (FIN) AF: 0.0521 AC: 553 AN: 10614

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0885 AC: 6021 AN: 68006

Other (OTH) AF: 0.101 AC: 213 AN: 2112

Alfa AF: 0.0893 Hom.: 1103

Bravo AF: 0.0946

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.63
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs10498071; hg19: chr2-220722698;