rs707552

Variant names:

• chr20-54343514-G-A
• rs707552

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 0.111 in 152,142 control chromosomes in the GnomAD database, including 2,959 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 0.11 (2959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.111 AC: 16897 AN: 152024 Hom.: 2956 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0591

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.00753

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00431

Gnomad OTH AF: 0.0749

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

GnomAD4 genome AF: 0.111 AC: 16919 AN: 152142 Hom.: 2959 Cov.: 32 AF XY: 0.108 AC XY: 8020 AN XY: 74388

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.0362

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0586

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.00753

Gnomad4 NFE AF: 0.00431

Gnomad4 OTH AF: 0.0750

Alfa AF: 0.0573 Hom.: 419

Bravo AF: 0.127

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.28
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs707552; hg19: chr20-52960053;