20-36982000-A-G

Variant names:

• chr20-36982000-A-G
• rs6124509

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 0.139 in 151,748 control chromosomes in the GnomAD database, including 2,198 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 0.14 (2198 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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: 0.139 AC: 21065 AN: 151628 Hom.: 2195 Cov.: 30

Gnomad AFR AF: 0.0389

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.139 AC: 21081 AN: 151748 Hom.: 2198 Cov.: 30 AF XY: 0.144 AC XY: 10686 AN XY: 74136

African (AFR) AF: 0.0391 AC: 1619 AN: 41430

American (AMR) AF: 0.180 AC: 2729 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2493 AN: 5100

South Asian (SAS) AF: 0.158 AC: 753 AN: 4780

European-Finnish (FIN) AF: 0.249 AC: 2621 AN: 10542

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9932 AN: 67938

Other (OTH) AF: 0.143 AC: 299 AN: 2098

Alfa AF: 0.0619 Hom.: 67

Bravo AF: 0.135

Asia WGS AF: 0.285 AC: 987 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.5
DANN	Benign	0.86
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs6124509; hg19: chr20-35610403;