rs1800686

Variant names:

• chr20-46117764-G-A
• rs1800686

Your query was ambiguous. Multiple possible variants found:

• chr20-46117764-G-A
• chr20-46117764-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0676 AC: 2806 AN: 41518

American (AMR) AF: 0.162 AC: 2475 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1492 AN: 5176

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4822

European-Finnish (FIN) AF: 0.247 AC: 2616 AN: 10590

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16464 AN: 67984

Other (OTH) AF: 0.193 AC: 408 AN: 2112

Alfa AF: 0.210 Hom.: 471

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1800686; hg19: chr20-44746403;