rs2223712

Variant names:

• chr20-11975011-G-A
• rs2223712

Your query was ambiguous. Multiple possible variants found:

• chr20-11975011-G-A
• chr20-11975011-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.799

Alfa AF: 0.801 Hom.: 5838

Bravo AF: 0.796

Asia WGS AF: 0.693 AC: 2412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2223712; hg19: chr20-11955659;