20-32752550-T-C

Variant names:

• chr20-32752550-T-C
• rs6141803

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 0.131 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
• Publications: 14 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0311 AC: 1292 AN: 41554

American (AMR) AF: 0.0828 AC: 1265 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1214 AN: 5168

South Asian (SAS) AF: 0.297 AC: 1432 AN: 4820

European-Finnish (FIN) AF: 0.165 AC: 1746 AN: 10606

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11627 AN: 67998

Other (OTH) AF: 0.130 AC: 275 AN: 2112

Alfa AF: 0.153 Hom.: 762

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
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs6141803; hg19: chr20-31340356;