rs563290

Variant names:

• chr2-21065354-G-A
• rs563290

Your query was ambiguous. Multiple possible variants found:

• chr2-21065354-G-A
• chr2-21065354-G-C

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 0.698 in 151,992 control chromosomes in the GnomAD database, including 40,060 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 0.70 (40060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.699 AC: 106097 AN: 151874 Hom.: 40058 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.698 AC: 106131 AN: 151992 Hom.: 40060 Cov.: 32 AF XY: 0.704 AC XY: 52315 AN XY: 74306

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.716

Alfa AF: 0.741 Hom.: 5458

Bravo AF: 0.683

Asia WGS AF: 0.894 AC: 3107 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs563290; hg19: chr2-21288226;