rs4851266

Positions:

• chr2-100202017-C-T

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 0.306 in 151,934 control chromosomes in the GnomAD database, including 8,484 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 0.31 (8484 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46528 AN: 151814 Hom.: 8488 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.327

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.306 AC: 46526 AN: 151934 Hom.: 8484 Cov.: 32 AF XY: 0.306 AC XY: 22710 AN XY: 74250

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.316

Alfa AF: 0.314 Hom.: 1614

Bravo AF: 0.292

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4851266; hg19: chr2-100818479; COSMIC: COSV53188249;