20-54193604-C-T

Variant names:

• chr20-54193604-C-T
• rs6068824

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 0.493 in 151,924 control chromosomes in the GnomAD database, including 19,820 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 (19820 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74954 AN: 151806 Hom.: 19818 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.493 AC: 74963 AN: 151924 Hom.: 19820 Cov.: 31 AF XY: 0.495 AC XY: 36757 AN XY: 74268

African (AFR) AF: 0.294 AC: 12194 AN: 41418

American (AMR) AF: 0.544 AC: 8310 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1689 AN: 5170

South Asian (SAS) AF: 0.592 AC: 2854 AN: 4818

European-Finnish (FIN) AF: 0.577 AC: 6077 AN: 10538

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40373 AN: 67934

Other (OTH) AF: 0.479 AC: 1009 AN: 2108

Alfa AF: 0.573 Hom.: 24462

Bravo AF: 0.480

Asia WGS AF: 0.462 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs6068824; hg19: chr20-52810143;