20-23374111-G-A

Variant names:

• chr20-23374111-G-A
• rs2252824

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 0.249 in 152,052 control chromosomes in the GnomAD database, including 5,416 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 0.25 (5416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 6 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 = 0.318 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: 0.249 AC: 37880 AN: 151934 Hom.: 5417 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.249 AC: 37877 AN: 152052 Hom.: 5416 Cov.: 32 AF XY: 0.253 AC XY: 18804 AN XY: 74288

African (AFR) AF: 0.0936 AC: 3885 AN: 41502

American (AMR) AF: 0.323 AC: 4940 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 959 AN: 3466

East Asian (EAS) AF: 0.332 AC: 1708 AN: 5152

South Asian (SAS) AF: 0.275 AC: 1327 AN: 4822

European-Finnish (FIN) AF: 0.297 AC: 3127 AN: 10542

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20899 AN: 67970

Other (OTH) AF: 0.266 AC: 560 AN: 2108

Alfa AF: 0.277 Hom.: 1067

Bravo AF: 0.247

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.18
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2252824; hg19: chr20-23354748;