rs234623

chr20-58913909-G-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 0.606 in 151,610 control chromosomes in the GnomAD database, including 30,500 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 0.61 (30500 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

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 = 0.889 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: 0.606 AC: 91839 AN: 151494 Hom.: 30445 Cov.: 30

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.606 AC: 91934 AN: 151610 Hom.: 30500 Cov.: 30 AF XY: 0.595 AC XY: 44027 AN XY: 73984

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.602

Alfa AF: 0.522 Hom.: 22456

Bravo AF: 0.631

Asia WGS AF: 0.445 AC: 1545 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	12
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs234623; hg19: chr20-57488964;