chr20-5865209-G-A

Variant names:

• chr20-5865209-G-A
• rs1699230

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 0.618 in 152,010 control chromosomes in the GnomAD database, including 29,356 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 0.62 (29356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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: 0.618 AC: 93931 AN: 151892 Hom.: 29348 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.618 AC: 93993 AN: 152010 Hom.: 29356 Cov.: 32 AF XY: 0.617 AC XY: 45827 AN XY: 74314

African (AFR) AF: 0.709 AC: 29393 AN: 41472

American (AMR) AF: 0.643 AC: 9831 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1760 AN: 3464

East Asian (EAS) AF: 0.708 AC: 3663 AN: 5172

South Asian (SAS) AF: 0.621 AC: 2990 AN: 4816

European-Finnish (FIN) AF: 0.542 AC: 5721 AN: 10554

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38734 AN: 67936

Other (OTH) AF: 0.615 AC: 1297 AN: 2110

Alfa AF: 0.578 Hom.: 47418

Bravo AF: 0.631

Asia WGS AF: 0.670 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.051
DANN	Benign	0.66
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1699230; hg19: chr20-5845855;