20-46000706-G-A

Variant names:

• chr20-46000706-G-A
• rs11697325

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.47 in 152,068 control chromosomes in the GnomAD database, including 18,705 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 0.47 (18705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.92
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71424 AN: 151948 Hom.: 18704 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.470 AC: 71434 AN: 152068 Hom.: 18705 Cov.: 32 AF XY: 0.461 AC XY: 34255 AN XY: 74312

African (AFR) AF: 0.292 AC: 12113 AN: 41468

American (AMR) AF: 0.513 AC: 7841 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1955 AN: 3470

East Asian (EAS) AF: 0.0336 AC: 174 AN: 5180

South Asian (SAS) AF: 0.338 AC: 1630 AN: 4820

European-Finnish (FIN) AF: 0.500 AC: 5287 AN: 10564

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40605 AN: 67962

Other (OTH) AF: 0.505 AC: 1066 AN: 2110

Alfa AF: 0.368 Hom.: 1007

Bravo AF: 0.460

Asia WGS AF: 0.186 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	21
DANN	Benign	0.85
PhyloP100		3.9

Splicing

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

Other links and lift over

dbSNP: rs11697325; hg19: chr20-44629345;