20-18099053-G-T

Variant names:

• chr20-18099053-G-T
• rs6111826

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 0.293 in 151,966 control chromosomes in the GnomAD database, including 7,175 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 0.29 (7175 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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: 0.293 AC: 44453 AN: 151848 Hom.: 7172 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.293 AC: 44477 AN: 151966 Hom.: 7175 Cov.: 31 AF XY: 0.297 AC XY: 22071 AN XY: 74274

African (AFR) AF: 0.140 AC: 5792 AN: 41492

American (AMR) AF: 0.385 AC: 5869 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1348 AN: 3462

East Asian (EAS) AF: 0.396 AC: 2035 AN: 5144

South Asian (SAS) AF: 0.358 AC: 1728 AN: 4822

European-Finnish (FIN) AF: 0.372 AC: 3927 AN: 10554

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22614 AN: 67936

Other (OTH) AF: 0.343 AC: 723 AN: 2108

Alfa AF: 0.311 Hom.: 11472

Bravo AF: 0.291

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6111826; hg19: chr20-18079697;