rs903228

Variant names:

• chr2-53464911-G-C
• rs903228

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 0.169 in 152,156 control chromosomes in the GnomAD database, including 3,338 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 0.17 (3338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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: 0.168 AC: 25587 AN: 152038 Hom.: 3313 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.169 AC: 25669 AN: 152156 Hom.: 3338 Cov.: 32 AF XY: 0.166 AC XY: 12355 AN XY: 74382

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0907

Gnomad4 SAS AF: 0.0866

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.176

Alfa AF: 0.132 Hom.: 264

Bravo AF: 0.189

Asia WGS AF: 0.106 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.91
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs903228; hg19: chr2-53692049;