rs2787093

chr20-3667815-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 0.868 in 152,194 control chromosomes in the GnomAD database, including 57,506 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 0.87 (57461 hom., cov: 32)
  • Exomes 𝑓: 0.83 (45 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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 (AMR) allele frequency at 95% confidence interval = 0.905 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: 0.868 AC: 131967 AN: 151950 Hom.: 57431 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.882

GnomAD4 exome AF: 0.833 AC: 105 AN: 126 Hom.: 45 AF XY: 0.824 AC XY: 84 AN XY: 102

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 SAS exome AF: 0.950

Gnomad4 FIN exome AF: 0.889

Gnomad4 NFE exome AF: 0.792

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.868 AC: 132051 AN: 152068 Hom.: 57461 Cov.: 32 AF XY: 0.866 AC XY: 64344 AN XY: 74326

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.880

Alfa AF: 0.880 Hom.: 11741

Bravo AF: 0.875

Asia WGS AF: 0.842 AC: 2927 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	4.3
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2787093; hg19: chr20-3648462;