20-56261298-T-C

Variant names:

• chr20-56261298-T-C
• rs913000

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 0.711 in 152,008 control chromosomes in the GnomAD database, including 38,635 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 0.71 (38635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 5 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 = 0.884 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: 0.711 AC: 107973 AN: 151890 Hom.: 38619 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.711 AC: 108032 AN: 152008 Hom.: 38635 Cov.: 32 AF XY: 0.713 AC XY: 52998 AN XY: 74286

African (AFR) AF: 0.668 AC: 27659 AN: 41432

American (AMR) AF: 0.788 AC: 12046 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2335 AN: 3468

East Asian (EAS) AF: 0.906 AC: 4679 AN: 5164

South Asian (SAS) AF: 0.776 AC: 3738 AN: 4818

European-Finnish (FIN) AF: 0.696 AC: 7331 AN: 10538

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47691 AN: 67986

Other (OTH) AF: 0.734 AC: 1550 AN: 2112

Alfa AF: 0.705 Hom.: 60663

Bravo AF: 0.717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.81
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs913000; hg19: chr20-54836354;