rs2324999

Positions:

• chr3-86109735-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 0.215 in 152,096 control chromosomes in the GnomAD database, including 3,543 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 0.21 (3543 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 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: 0.215 AC: 32621 AN: 151978 Hom.: 3545 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.215 AC: 32627 AN: 152096 Hom.: 3543 Cov.: 33 AF XY: 0.217 AC XY: 16091 AN XY: 74322

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.216

Alfa AF: 0.204 Hom.: 4093

Bravo AF: 0.214

Asia WGS AF: 0.252 AC: 872 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2324999; hg19: chr3-86158885;