chr20-9938924-A-G

Variant names:

• chr20-9938924-A-G
• rs6118819

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 0.363 in 152,088 control chromosomes in the GnomAD database, including 10,774 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 0.36 (10774 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.641
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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: 0.363 AC: 55156 AN: 151970 Hom.: 10759 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.363 AC: 55191 AN: 152088 Hom.: 10774 Cov.: 33 AF XY: 0.370 AC XY: 27511 AN XY: 74326

African (AFR) AF: 0.233 AC: 9685 AN: 41530

American (AMR) AF: 0.463 AC: 7063 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3468

East Asian (EAS) AF: 0.510 AC: 2633 AN: 5162

South Asian (SAS) AF: 0.465 AC: 2241 AN: 4818

European-Finnish (FIN) AF: 0.447 AC: 4731 AN: 10588

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26546 AN: 67950

Other (OTH) AF: 0.344 AC: 724 AN: 2106

Alfa AF: 0.313 Hom.: 1356

Bravo AF: 0.357

Asia WGS AF: 0.484 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.72
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs6118819; hg19: chr20-9919572;