rs1522813

Variant names:

• chr2-226080466-G-A
• rs1522813

Your query was ambiguous. Multiple possible variants found:

• chr2-226080466-G-A
• chr2-226080466-G-C

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 0.289 in 152,052 control chromosomes in the GnomAD database, including 6,496 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 0.29 (6496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 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: 0.289 AC: 43932 AN: 151934 Hom.: 6480 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.289 AC: 43985 AN: 152052 Hom.: 6496 Cov.: 32 AF XY: 0.293 AC XY: 21772 AN XY: 74352

African (AFR) AF: 0.309 AC: 12792 AN: 41460

American (AMR) AF: 0.340 AC: 5198 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1296 AN: 3472

East Asian (EAS) AF: 0.360 AC: 1861 AN: 5164

South Asian (SAS) AF: 0.368 AC: 1775 AN: 4818

European-Finnish (FIN) AF: 0.240 AC: 2541 AN: 10570

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17644 AN: 67972

Other (OTH) AF: 0.270 AC: 571 AN: 2114

Alfa AF: 0.274 Hom.: 717

Bravo AF: 0.292

Asia WGS AF: 0.433 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.36
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1522813; hg19: chr2-226945182;