rs3820897

Positions:

• chr2-3594771-T-C

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 0.782 in 215,862 control chromosomes in the GnomAD database, including 68,465 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 0.80 (50472 hom., cov: 32)
  • Exomes 𝑓: 0.73 (17993 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121917 AN: 152034 Hom.: 50427 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.819

GnomAD4 exome AF: 0.734 AC: 46765 AN: 63708 Hom.: 17993 AF XY: 0.708 AC XY: 24917 AN XY: 35206

Gnomad4 AFR exome AF: 0.926

Gnomad4 AMR exome AF: 0.752

Gnomad4 ASJ exome AF: 0.849

Gnomad4 EAS exome AF: 0.263

Gnomad4 SAS exome AF: 0.553

Gnomad4 FIN exome AF: 0.643

Gnomad4 NFE exome AF: 0.818

Gnomad4 OTH exome AF: 0.760

GnomAD4 genome AF: 0.802 AC: 122014 AN: 152154 Hom.: 50472 Cov.: 32 AF XY: 0.784 AC XY: 58282 AN XY: 74374

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.811

Alfa AF: 0.809 Hom.: 80902

Bravo AF: 0.820

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.1
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: rs3820897; hg19: chr2-3642361;