rs1522928

Variant names:

• chr2-73298409-C-T
• rs1522928

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 0.23 in 152,052 control chromosomes in the GnomAD database, including 7,546 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 0.23 (7546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.229 AC: 34807 AN: 151934 Hom.: 7510 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0589

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.230 AC: 34906 AN: 152052 Hom.: 7546 Cov.: 32 AF XY: 0.230 AC XY: 17095 AN XY: 74358

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.0552

Gnomad4 NFE AF: 0.0589

Gnomad4 OTH AF: 0.200

Alfa AF: 0.0960 Hom.: 1994

Bravo AF: 0.259

Asia WGS AF: 0.331 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.79
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1522928; hg19: chr2-73525537;