20-45999741-C-T

Variant names:

• chr20-45999741-C-T
• rs11696804

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.47 in 152,052 control chromosomes in the GnomAD database, including 18,717 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 0.47 (18717 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 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: 0.470 AC: 71444 AN: 151936 Hom.: 18717 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.470 AC: 71451 AN: 152052 Hom.: 18717 Cov.: 32 AF XY: 0.461 AC XY: 34271 AN XY: 74308

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.0336

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.506

Alfa AF: 0.439 Hom.: 2160

Bravo AF: 0.460

Asia WGS AF: 0.186 AC: 650 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	7.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11696804; hg19: chr20-44628380;