rs2092380

Variant names:

• chr20-7775380-G-A
• rs2092380

Your query was ambiguous. Multiple possible variants found:

• chr20-7775380-G-A
• chr20-7775380-G-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 0.108 in 152,030 control chromosomes in the GnomAD database, including 1,050 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 0.11 (1050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.294 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: 0.108 AC: 16386 AN: 151912 Hom.: 1044 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.0615

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.108 AC: 16400 AN: 152030 Hom.: 1050 Cov.: 32 AF XY: 0.110 AC XY: 8142 AN XY: 74296

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.0615

Gnomad4 NFE AF: 0.0895

Gnomad4 OTH AF: 0.135

Alfa AF: 0.103 Hom.: 1345

Bravo AF: 0.113

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
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: rs2092380; hg19: chr20-7756027;