20-53513125-A-C

Variant names:

• chr20-53513125-A-C
• rs1326861

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 0.493 in 150,962 control chromosomes in the GnomAD database, including 18,542 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 0.49 (18542 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 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: 0.493 AC: 74414 AN: 150846 Hom.: 18522 Cov.: 28

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.493 AC: 74475 AN: 150962 Hom.: 18542 Cov.: 28 AF XY: 0.494 AC XY: 36421 AN XY: 73676

African (AFR) AF: 0.505 AC: 20721 AN: 41026

American (AMR) AF: 0.467 AC: 7071 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1633 AN: 3462

East Asian (EAS) AF: 0.442 AC: 2252 AN: 5098

South Asian (SAS) AF: 0.427 AC: 2037 AN: 4768

European-Finnish (FIN) AF: 0.600 AC: 6225 AN: 10376

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 32971 AN: 67782

Other (OTH) AF: 0.483 AC: 1011 AN: 2094

Alfa AF: 0.485 Hom.: 2789

Bravo AF: 0.485

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.39
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1326861; hg19: chr20-52129664;