rs2224703

Variant names:

• chr20-12350627-G-A
• rs2224703

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 0.173 in 151,846 control chromosomes in the GnomAD database, including 2,727 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 0.17 (2727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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: 0.174 AC: 26337 AN: 151728 Hom.: 2726 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.173 AC: 26336 AN: 151846 Hom.: 2727 Cov.: 32 AF XY: 0.178 AC XY: 13234 AN XY: 74224

African (AFR) AF: 0.0562 AC: 2330 AN: 41438

American (AMR) AF: 0.233 AC: 3557 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1777 AN: 5152

South Asian (SAS) AF: 0.136 AC: 654 AN: 4816

European-Finnish (FIN) AF: 0.235 AC: 2470 AN: 10512

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14218 AN: 67910

Other (OTH) AF: 0.167 AC: 352 AN: 2106

Alfa AF: 0.182 Hom.: 358

Bravo AF: 0.170

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.84
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2224703; hg19: chr20-12331275;