rs2424635

chr20-24736449-C-A

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 0.52 in 152,190 control chromosomes in the GnomAD database, including 22,103 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 0.52 (22103 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 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: 0.521 AC: 79191 AN: 152072 Hom.: 22109 Cov.: 34

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.520 AC: 79203 AN: 152190 Hom.: 22103 Cov.: 34 AF XY: 0.519 AC XY: 38619 AN XY: 74410

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.512

Alfa AF: 0.558 Hom.: 3911

Bravo AF: 0.498

Asia WGS AF: 0.315 AC: 1096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.9
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2424635; hg19: chr20-24717085;