rs3096851

Positions:

• chr2-203899159-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;