chr3-99377052-C-T

Variant names:

• chr3-99377052-C-T
• rs2200019

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 0.302 in 152,040 control chromosomes in the GnomAD database, including 7,041 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 0.30 (7041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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: 0.301 AC: 45798 AN: 151922 Hom.: 7021 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.302 AC: 45872 AN: 152040 Hom.: 7041 Cov.: 32 AF XY: 0.302 AC XY: 22461 AN XY: 74318

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.305

Alfa AF: 0.294 Hom.: 3555

Bravo AF: 0.298

Asia WGS AF: 0.346 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2200019; hg19: chr3-99095896;