chr20-32752550-T-C

Position:

• chr20-32752550-T-C

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 0.131 in 152,208 control chromosomes in the GnomAD database, including 1,754 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 0.13 (1754 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20005 AN: 152090 Hom.: 1751 Cov.: 32

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.131 AC: 19995 AN: 152208 Hom.: 1754 Cov.: 32 AF XY: 0.136 AC XY: 10102 AN XY: 74436

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.0828

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.130

Alfa AF: 0.149 Hom.: 395

Bravo AF: 0.116

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.8
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: rs6141803; hg19: chr20-31340356;