rs2423302

Variant names:

• chr20-7843207-G-A
• rs2423302

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 0.277 in 151,880 control chromosomes in the GnomAD database, including 6,065 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 0.28 (6065 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 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: 0.277 AC: 42050 AN: 151760 Hom.: 6054 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.277 AC: 42102 AN: 151880 Hom.: 6065 Cov.: 32 AF XY: 0.277 AC XY: 20540 AN XY: 74214

African (AFR) AF: 0.299 AC: 12362 AN: 41392

American (AMR) AF: 0.299 AC: 4569 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3470

East Asian (EAS) AF: 0.325 AC: 1672 AN: 5150

South Asian (SAS) AF: 0.485 AC: 2325 AN: 4794

European-Finnish (FIN) AF: 0.205 AC: 2161 AN: 10550

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.248 AC: 16863 AN: 67950

Other (OTH) AF: 0.302 AC: 636 AN: 2108

Alfa AF: 0.258 Hom.: 2252

Bravo AF: 0.284

Asia WGS AF: 0.441 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.34
DANN	Benign	0.61
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2423302; hg19: chr20-7823854;