20-55933455-T-G

Variant names:

• chr20-55933455-T-G
• rs4811645

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 0.487 in 151,978 control chromosomes in the GnomAD database, including 18,978 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 0.49 (18978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 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: 0.487 AC: 73982 AN: 151860 Hom.: 18972 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.487 AC: 74023 AN: 151978 Hom.: 18978 Cov.: 32 AF XY: 0.494 AC XY: 36696 AN XY: 74286

African (AFR) AF: 0.367 AC: 15191 AN: 41446

American (AMR) AF: 0.586 AC: 8945 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4519 AN: 5156

South Asian (SAS) AF: 0.634 AC: 3053 AN: 4818

European-Finnish (FIN) AF: 0.545 AC: 5751 AN: 10552

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33589 AN: 67954

Other (OTH) AF: 0.470 AC: 993 AN: 2114

Alfa AF: 0.489 Hom.: 57317

Bravo AF: 0.485

Asia WGS AF: 0.711 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.77
DANN	Benign	0.82
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs4811645; hg19: chr20-54508511;