rs3849399

Variant names:

• chr2-22688855-T-C
• rs3849399

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 0.0721 in 152,256 control chromosomes in the GnomAD database, including 373 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 0.072 (373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0982 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: 0.0721 AC: 10970 AN: 152138 Hom.: 373 Cov.: 32

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0721 AC: 10974 AN: 152256 Hom.: 373 Cov.: 32 AF XY: 0.0740 AC XY: 5511 AN XY: 74434

Gnomad4 AFR AF: 0.0628

Gnomad4 AMR AF: 0.0494

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.0820

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0737

Gnomad4 OTH AF: 0.0635

Alfa AF: 0.0765 Hom.: 265

Bravo AF: 0.0653

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3849399; hg19: chr2-22911727;