rs210069

Variant names:

• chr20-54112406-C-T
• rs210069

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 152,092 control chromosomes in the GnomAD database, including 7,362 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 (7362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

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 (EAS) allele frequency at 95% confidence interval = 0.451 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: 47137 AN: 151974 Hom.: 7356 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.310 AC: 47167 AN: 152092 Hom.: 7362 Cov.: 32 AF XY: 0.309 AC XY: 22998 AN XY: 74358

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.302

Alfa AF: 0.298 Hom.: 14184

Bravo AF: 0.316

Asia WGS AF: 0.377 AC: 1312 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	0.64
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs210069; hg19: chr20-52728945;