20-11975011-G-A

Variant names:

• chr20-11975011-G-A
• rs2223712

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 0.796 in 152,048 control chromosomes in the GnomAD database, including 48,639 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 0.80 (48639 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 2 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 (AMR) allele frequency at 95% confidence interval = 0.856 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: 0.796 AC: 121012 AN: 151930 Hom.: 48604 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.796 AC: 121092 AN: 152048 Hom.: 48639 Cov.: 31 AF XY: 0.794 AC XY: 59020 AN XY: 74312

African (AFR) AF: 0.714 AC: 29598 AN: 41452

American (AMR) AF: 0.868 AC: 13260 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2608 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3157 AN: 5132

South Asian (SAS) AF: 0.705 AC: 3397 AN: 4818

European-Finnish (FIN) AF: 0.861 AC: 9106 AN: 10570

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57300 AN: 68012

Other (OTH) AF: 0.799 AC: 1690 AN: 2116

Alfa AF: 0.799 Hom.: 6056

Bravo AF: 0.796

Asia WGS AF: 0.693 AC: 2412 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	0.35
DANN	Benign	0.38
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2223712; hg19: chr20-11955659;