20-21993952-T-C

Variant names:

• chr20-21993952-T-C
• rs6036007

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 0.531 in 151,906 control chromosomes in the GnomAD database, including 22,400 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 0.53 (22400 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80515 AN: 151788 Hom.: 22344 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.531 AC: 80629 AN: 151906 Hom.: 22400 Cov.: 31 AF XY: 0.528 AC XY: 39191 AN XY: 74236

African (AFR) AF: 0.684 AC: 28354 AN: 41460

American (AMR) AF: 0.629 AC: 9603 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1636 AN: 3464

East Asian (EAS) AF: 0.507 AC: 2592 AN: 5110

South Asian (SAS) AF: 0.508 AC: 2443 AN: 4806

European-Finnish (FIN) AF: 0.376 AC: 3970 AN: 10558

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30270 AN: 67926

Other (OTH) AF: 0.545 AC: 1152 AN: 2112

Alfa AF: 0.489 Hom.: 2360

Bravo AF: 0.558

Asia WGS AF: 0.579 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.27
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs6036007; hg19: chr20-21974590;