2-21048451-A-G

Variant names:

• chr2-21048451-A-G
• rs1713222

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 0.821 in 152,026 control chromosomes in the GnomAD database, including 51,638 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 0.82 (51638 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.821 AC: 124740 AN: 151908 Hom.: 51590 Cov.: 30

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.821 AC: 124842 AN: 152026 Hom.: 51638 Cov.: 30 AF XY: 0.823 AC XY: 61164 AN XY: 74292

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.852

Gnomad4 OTH AF: 0.816

Alfa AF: 0.815 Hom.: 4896

Bravo AF: 0.816

Asia WGS AF: 0.937 AC: 3259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1713222; hg19: chr2-21271323;