rs234623

Variant names:

• chr20-58913909-G-A
• rs234623

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.897 AC: 37140 AN: 41400

American (AMR) AF: 0.525 AC: 7991 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2167 AN: 3466

East Asian (EAS) AF: 0.461 AC: 2382 AN: 5164

South Asian (SAS) AF: 0.397 AC: 1908 AN: 4806

European-Finnish (FIN) AF: 0.383 AC: 3956 AN: 10336

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.509 AC: 34555 AN: 67900

Other (OTH) AF: 0.602 AC: 1268 AN: 2106

Alfa AF: 0.526 Hom.: 26729

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
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs234623; hg19: chr20-57488964;