chr20-54798000-T-G

Variant names:

• chr20-54798000-T-G
• rs157640

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 0.454 in 152,002 control chromosomes in the GnomAD database, including 17,657 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 0.45 (17657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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: 0.454 AC: 68927 AN: 151884 Hom.: 17655 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.454 AC: 68934 AN: 152002 Hom.: 17657 Cov.: 32 AF XY: 0.460 AC XY: 34180 AN XY: 74310

African (AFR) AF: 0.196 AC: 8122 AN: 41492

American (AMR) AF: 0.467 AC: 7110 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1925 AN: 3468

East Asian (EAS) AF: 0.632 AC: 3268 AN: 5170

South Asian (SAS) AF: 0.494 AC: 2380 AN: 4814

European-Finnish (FIN) AF: 0.633 AC: 6686 AN: 10570

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37810 AN: 67954

Other (OTH) AF: 0.479 AC: 1009 AN: 2106

Alfa AF: 0.531 Hom.: 36595

Bravo AF: 0.429

Asia WGS AF: 0.541 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.6
DANN	Benign	0.26
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs157640; hg19: chr20-53414539;