rs2851300

Variant names:

• chr4-99358667-C-T
• rs2851300

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 0.314 in 151,950 control chromosomes in the GnomAD database, including 8,919 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 (8919 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47709 AN: 151832 Hom.: 8912 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.314 AC: 47732 AN: 151950 Hom.: 8919 Cov.: 33 AF XY: 0.315 AC XY: 23388 AN XY: 74254

African (AFR) AF: 0.144 AC: 5979 AN: 41424

American (AMR) AF: 0.294 AC: 4491 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 991 AN: 3462

East Asian (EAS) AF: 0.0820 AC: 425 AN: 5184

South Asian (SAS) AF: 0.308 AC: 1485 AN: 4820

European-Finnish (FIN) AF: 0.516 AC: 5414 AN: 10502

Middle Eastern (MID) AF: 0.234 AC: 68 AN: 290

European-Non Finnish (NFE) AF: 0.413 AC: 28064 AN: 67974

Other (OTH) AF: 0.287 AC: 606 AN: 2108

Alfa AF: 0.367 Hom.: 17792

Bravo AF: 0.288

Asia WGS AF: 0.222 AC: 769 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.59
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2851300; hg19: chr4-100279824;