rs1800686

Positions:

• chr20-46117764-G-A
• chr20-46117764-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 0.192 in 152,166 control chromosomes in the GnomAD database, including 3,338 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 0.19 (3338 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 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: 0.192 AC: 29183 AN: 152048 Hom.: 3334 Cov.: 33

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.192 AC: 29195 AN: 152166 Hom.: 3338 Cov.: 33 AF XY: 0.194 AC XY: 14421 AN XY: 74384

Gnomad4 AFR AF: 0.0676

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.193

Alfa AF: 0.215 Hom.: 468

Bravo AF: 0.180

Asia WGS AF: 0.239 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.6
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800686; hg19: chr20-44746403;