rs224788

Positions:

• chr20-24259293-G-C
• chr20-24259293-G-T

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 0.655 in 152,134 control chromosomes in the GnomAD database, including 33,499 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 0.65 (33499 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 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: 0.655 AC: 99552 AN: 152016 Hom.: 33462 Cov.: 33

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.655 AC: 99647 AN: 152134 Hom.: 33499 Cov.: 33 AF XY: 0.656 AC XY: 48781 AN XY: 74376

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.627

Alfa AF: 0.634 Hom.: 3900

Bravo AF: 0.643

Asia WGS AF: 0.523 AC: 1822 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	0.055
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: rs224788; hg19: chr20-24239929;