rs2851300

Variant names:

• chr4-99358667-C-T
• rs2851300

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 0.314 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.314 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

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.0820

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.287

Alfa AF: 0.377 Hom.: 14573

Bravo AF: 0.288

Asia WGS AF: 0.222 AC: 769 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2851300; hg19: chr4-100279824;