20-23288000-T-C

Variant names:

• chr20-23288000-T-C
• rs4815191

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 0.761 in 152,160 control chromosomes in the GnomAD database, including 44,942 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 0.76 (44942 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115623 AN: 152042 Hom.: 44889 Cov.: 33

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.761 AC: 115737 AN: 152160 Hom.: 44942 Cov.: 33 AF XY: 0.765 AC XY: 56935 AN XY: 74382

African (AFR) AF: 0.909 AC: 37712 AN: 41510

American (AMR) AF: 0.737 AC: 11267 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2460 AN: 3472

East Asian (EAS) AF: 0.856 AC: 4427 AN: 5170

South Asian (SAS) AF: 0.838 AC: 4035 AN: 4816

European-Finnish (FIN) AF: 0.775 AC: 8221 AN: 10602

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45316 AN: 67976

Other (OTH) AF: 0.733 AC: 1549 AN: 2112

Alfa AF: 0.698 Hom.: 143152

Bravo AF: 0.763

Asia WGS AF: 0.838 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.68
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4815191; hg19: chr20-23268637; COSMIC: COSV69623697;