rs2423297

chr20-7840844-G-Achr20-7840844-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 0.336 in 151,920 control chromosomes in the GnomAD database, including 9,673 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 0.34 (9673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50993 AN: 151802 Hom.: 9645 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.336 AC: 51077 AN: 151920 Hom.: 9673 Cov.: 32 AF XY: 0.334 AC XY: 24798 AN XY: 74272

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.348

Alfa AF: 0.279 Hom.: 1522

Bravo AF: 0.352

Asia WGS AF: 0.454 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2423297; hg19: chr20-7821491;