rs4851266

Variant names:

• chr2-100202017-C-T
• rs4851266

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.113 AC: 4704 AN: 41472

American (AMR) AF: 0.305 AC: 4649 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3466

East Asian (EAS) AF: 0.559 AC: 2872 AN: 5138

South Asian (SAS) AF: 0.258 AC: 1235 AN: 4794

European-Finnish (FIN) AF: 0.413 AC: 4360 AN: 10558

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.395 AC: 26841 AN: 67922

Other (OTH) AF: 0.316 AC: 668 AN: 2116

Alfa AF: 0.354 Hom.: 17337

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
PhyloP100		-0.084

Splicing

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

Other links and lift over

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