rs3783557

Variant names:

• chr2-112773135-C-T
• rs3783557

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 0.203 in 151,928 control chromosomes in the GnomAD database, including 4,094 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 0.20 (4094 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 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: 0.203 AC: 30782 AN: 151810 Hom.: 4094 Cov.: 31

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.203 AC: 30780 AN: 151928 Hom.: 4094 Cov.: 31 AF XY: 0.202 AC XY: 14994 AN XY: 74252

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.0311

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.214

Alfa AF: 0.236 Hom.: 1034

Bravo AF: 0.183

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.094
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3783557; hg19: chr2-113530712;