rs3096851

Variant names:

• chr2-203899159-A-C
• rs3096851

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 0.371 in 151,824 control chromosomes in the GnomAD database, including 10,952 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 0.37 (10952 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 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: 0.371 AC: 56244 AN: 151706 Hom.: 10940 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.371 AC: 56303 AN: 151824 Hom.: 10952 Cov.: 31 AF XY: 0.376 AC XY: 27923 AN XY: 74188

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.320

Alfa AF: 0.326 Hom.: 5381

Bravo AF: 0.369

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3096851; hg19: chr2-204763882;