rs2423302

Variant names:

• chr20-7843207-G-A
• rs2423302

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 0.277 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.302

Alfa AF: 0.260 Hom.: 1244

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2423302; hg19: chr20-7823854;