rs234621

Variant names:

• chr20-58915193-C-A
• rs234621

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 0.31 in 152,042 control chromosomes in the GnomAD database, including 7,262 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 0.31 (7262 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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: 0.310 AC: 47042 AN: 151924 Hom.: 7252 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.310 AC: 47061 AN: 152042 Hom.: 7262 Cov.: 32 AF XY: 0.308 AC XY: 22891 AN XY: 74308

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.304

Alfa AF: 0.305 Hom.: 14667

Bravo AF: 0.310

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.097
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs234621; hg19: chr20-57490248;