20-53839906-T-G

Variant names:

• chr20-53839906-T-G
• rs6126982

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 0.537 in 152,120 control chromosomes in the GnomAD database, including 22,045 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 0.54 (22045 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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: 0.537 AC: 81572 AN: 152002 Hom.: 22037 Cov.: 33

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.537 AC: 81618 AN: 152120 Hom.: 22045 Cov.: 33 AF XY: 0.539 AC XY: 40105 AN XY: 74394

African (AFR) AF: 0.563 AC: 23339 AN: 41486

American (AMR) AF: 0.583 AC: 8906 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1728 AN: 3468

East Asian (EAS) AF: 0.626 AC: 3233 AN: 5162

South Asian (SAS) AF: 0.470 AC: 2272 AN: 4832

European-Finnish (FIN) AF: 0.566 AC: 5999 AN: 10596

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.509 AC: 34593 AN: 67984

Other (OTH) AF: 0.533 AC: 1125 AN: 2112

Alfa AF: 0.518 Hom.: 67345

Bravo AF: 0.540

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6126982; hg19: chr20-52456445;