rs1528216

Variant names:

• chr2-228338114-A-T
• rs1528216

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 0.206 in 152,152 control chromosomes in the GnomAD database, including 4,045 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 0.21 (4045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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: 0.206 AC: 31302 AN: 152036 Hom.: 4045 Cov.: 32

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.206 AC: 31294 AN: 152152 Hom.: 4045 Cov.: 32 AF XY: 0.206 AC XY: 15312 AN XY: 74388

Gnomad4 AFR AF: 0.0566

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.221

Alfa AF: 0.234 Hom.: 581

Bravo AF: 0.197

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1528216; hg19: chr2-229202830;