20-32760944-C-T

Variant names:

• chr20-32760944-C-T
• rs6058869

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 0.549 in 152,068 control chromosomes in the GnomAD database, including 25,601 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 0.55 (25601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.549 AC: 83426 AN: 151950 Hom.: 25564 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.549 AC: 83515 AN: 152068 Hom.: 25601 Cov.: 32 AF XY: 0.554 AC XY: 41180 AN XY: 74326

African (AFR) AF: 0.786 AC: 32629 AN: 41498

American (AMR) AF: 0.565 AC: 8628 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1532 AN: 3468

East Asian (EAS) AF: 0.924 AC: 4774 AN: 5166

South Asian (SAS) AF: 0.656 AC: 3165 AN: 4826

European-Finnish (FIN) AF: 0.404 AC: 4273 AN: 10574

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26935 AN: 67944

Other (OTH) AF: 0.493 AC: 1042 AN: 2112

Alfa AF: 0.472 Hom.: 14624

Bravo AF: 0.573

Asia WGS AF: 0.743 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.49
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs6058869; hg19: chr20-31348750;